I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 9 13:54:57 +14 2025 I: pbuilder-time-stamp: 1739058897 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/1451124/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. 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 Feb 8 23:55 /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/1451124/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1451124/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=4c443f5a90a044c296dd20b84d8e4d80 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=1451124 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.0km5zLHM/pbuilderrc_V5RN --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.0km5zLHM/b2 --logfile b2/build.log gromacs_2022.5-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.104:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash -rwxr-xr-x 3 root root 67728 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67728 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 67728 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67664 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 68536 Sep 20 2022 cat -rwxr-xr-x 1 root root 68616 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 68552 Sep 20 2022 chmod -rwxr-xr-x 1 root root 68632 Sep 20 2022 chown -rwxr-xr-x 1 root root 200264 Sep 20 2022 cp -rwxr-xr-x 1 root root 133640 Jan 5 2023 dash -rwxr-xr-x 1 root root 134144 Sep 20 2022 date -rwxr-xr-x 1 root root 134248 Sep 20 2022 dd -rwxr-xr-x 1 root root 134888 Sep 20 2022 df -rwxr-xr-x 1 root root 200440 Sep 20 2022 dir -rwxr-xr-x 1 root root 141720 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 68408 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 68384 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 134584 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 67744 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 198880 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 93752 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67592 Dec 19 2022 hostname -rwxr-xr-x 1 root root 68664 Sep 20 2022 ln -rwxr-xr-x 1 root root 69208 Mar 23 2023 login -rwxr-xr-x 1 root root 200440 Sep 20 2022 ls -rwxr-xr-x 1 root root 264360 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 134384 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 68768 Sep 20 2022 mknod -rwxr-xr-x 1 root root 68472 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 67752 Mar 23 2023 more -rwsr-xr-x 1 root root 67744 Mar 23 2023 mount -rwxr-xr-x 1 root root 67744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 134728 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 68496 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 68456 Sep 20 2022 readlink -rwxr-xr-x 1 root root 68592 Sep 20 2022 rm -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 68392 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed lrwxrwxrwx 1 root root 9 Feb 8 23:55 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su -rwxr-xr-x 1 root root 68448 Sep 20 2022 sync -rwxr-xr-x 1 root root 539896 Apr 6 2023 tar -rwxr-xr-x 1 root root 67904 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 134160 Sep 20 2022 touch -rwxr-xr-x 1 root root 68384 Sep 20 2022 true -rwxr-xr-x 1 root root 67664 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 67744 Mar 23 2023 umount -rwxr-xr-x 1 root root 68416 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 200440 Sep 20 2022 vdir -rwxr-xr-x 1 root root 133312 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/1451124/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: arm64 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 ... 18171 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-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} 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} 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, 286 newly installed, 0 to remove and 0 not upgraded. Need to get 268 MB of archives. After unpacking 1193 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 12 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 sgml-base all 1.31 [15.4 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 tzdata all 2023c-5+deb12u1 [296 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 bash-completion all 1:2.11-6 [234 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.11-1~deb12u2 [1385 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libcbor0.8 arm64 0.8.0-2+b1 [26.0 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libfido2-1 arm64 1.12.0-2+b1 [72.6 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 openssh-client arm64 1:9.2p1-2+deb12u1 [935 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.3~deb12u1 [619 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1+deb12u1 [68.3 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-10+deb12u4 [366 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libz3-4 arm64 4.8.12-3.1 [6282 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libllvm14 arm64 1:14.0.6-12 [19.3 MB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libclang-cpp14 arm64 1:14.0.6-12 [9866 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libclang1-14 arm64 1:14.0.6-12 [5465 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 doxygen arm64 1.9.4-4 [4216 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-5 [369 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libfontenc1 arm64 1:1.1.4-1 [23.6 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 fontconfig arm64 2.14.1-4 [449 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libgfortran-12-dev arm64 12.2.0-14 [396 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 gfortran-12 arm64 12.2.0-14 [8646 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libgs-common all 10.0.0~dfsg-11+deb12u2 [148 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libgs10-common all 10.0.0~dfsg-11+deb12u2 [586 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libavahi-common-data arm64 0.8-10 [107 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libavahi-common3 arm64 0.8-10 [40.6 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libdbus-1-3 arm64 1.14.10-1~deb12u1 [193 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libavahi-client3 arm64 0.8-10 [43.8 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libcups2 arm64 2.4.2-3+deb12u5 [229 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 libidn12 arm64 1.41-1 [82.8 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libijs-0.35 arm64 0.35-15 [15.8 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libjbig2dec0 arm64 0.19-3 [62.8 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 libopenjp2-7 arm64 2.5.0-2 [175 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 libpaper1 arm64 1.1.29 [12.6 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.2+deb12u1 [260 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-6+deb12u1 [301 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2+deb12u2 [735 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libxt6 arm64 1:1.2.1-1.1 [172 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 libgs10 arm64 10.0.0~dfsg-11+deb12u2 [2253 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 ghostscript arm64 10.0.0~dfsg-11+deb12u2 [57.0 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libaom3 arm64 3.6.0-1 [1379 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libdav1d6 arm64 1.0.0-2 [274 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 libde265-0 arm64 1.0.11-1+deb12u1 [148 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 libnuma1 arm64 2.0.16-1 [20.3 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libx265-199 arm64 3.5-2+b1 [603 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libheif1 arm64 1.15.1-1 [191 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libhwy1 arm64 1.0.3-3+deb12u1 [226 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libjxl0.7 arm64 0.7.0-10 [643 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 libwebpmux3 arm64 1.2.4-0.2+deb12u1 [109 kB] Get: 131 http://deb.debian.org/debian bookworm/main arm64 libwmflite-0.2-7 arm64 0.2.12-5.1 [71.0 kB] Get: 132 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 133 http://deb.debian.org/debian bookworm/main arm64 libgraphicsmagick-q16-3 arm64 1.4+really1.3.40-4 [1030 kB] Get: 134 http://deb.debian.org/debian bookworm/main arm64 graphicsmagick arm64 1.4+really1.3.40-4 [1020 kB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 libann0 arm64 1.1.2+doc-9+b1 [23.6 kB] Get: 136 http://deb.debian.org/debian bookworm/main arm64 libcdt5 arm64 2.42.2-7+b3 [38.6 kB] Get: 137 http://deb.debian.org/debian bookworm/main arm64 libcgraph6 arm64 2.42.2-7+b3 [60.0 kB] Get: 138 http://deb.debian.org/debian bookworm/main arm64 libabsl20220623 arm64 20220623.1-1 [363 kB] Get: 139 http://deb.debian.org/debian bookworm/main arm64 libgav1-1 arm64 0.18.0-1+b1 [425 kB] Get: 140 http://deb.debian.org/debian bookworm/main arm64 librav1e0 arm64 0.5.1-6 [552 kB] Get: 141 http://deb.debian.org/debian bookworm/main arm64 libsvtav1enc1 arm64 1.4.1+dfsg-1 [1074 kB] Get: 142 http://deb.debian.org/debian bookworm/main arm64 libyuv0 arm64 0.0~git20230123.b2528b0-1 [122 kB] Get: 143 http://deb.debian.org/debian bookworm/main arm64 libavif15 arm64 0.11.1-1 [88.3 kB] Get: 144 http://deb.debian.org/debian bookworm/main arm64 libxpm4 arm64 1:3.5.12-1.1+deb12u1 [45.4 kB] Get: 145 http://deb.debian.org/debian bookworm/main arm64 libgd3 arm64 2.3.3-9 [113 kB] Get: 146 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-2 [1310 kB] Get: 147 http://deb.debian.org/debian bookworm/main arm64 libgts-0.7-5 arm64 0.7.6+darcs121130-5+b1 [142 kB] Get: 148 http://deb.debian.org/debian bookworm/main arm64 libpixman-1-0 arm64 0.42.2-1 [470 kB] Get: 149 http://deb.debian.org/debian bookworm/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 150 http://deb.debian.org/debian bookworm/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 151 http://deb.debian.org/debian bookworm/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB] Get: 152 http://deb.debian.org/debian bookworm/main arm64 libcairo2 arm64 1.16.0-7 [527 kB] Get: 153 http://deb.debian.org/debian bookworm/main arm64 libltdl7 arm64 2.4.7-5 [392 kB] Get: 154 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB] Get: 155 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 156 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 libthai-data all 0.1.29-1 [176 kB] Get: 158 http://deb.debian.org/debian bookworm/main arm64 libdatrie1 arm64 0.2.13-2+b1 [42.6 kB] Get: 159 http://deb.debian.org/debian bookworm/main arm64 libthai0 arm64 0.1.29-1 [56.2 kB] Get: 160 http://deb.debian.org/debian bookworm/main arm64 libpango-1.0-0 arm64 1.50.12+ds-1 [200 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 libpangoft2-1.0-0 arm64 1.50.12+ds-1 [44.5 kB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 libpangocairo-1.0-0 arm64 1.50.12+ds-1 [32.0 kB] Get: 163 http://deb.debian.org/debian bookworm/main arm64 libpathplan4 arm64 2.42.2-7+b3 [40.4 kB] Get: 164 http://deb.debian.org/debian bookworm/main arm64 libgvc6 arm64 2.42.2-7+b3 [613 kB] Get: 165 http://deb.debian.org/debian bookworm/main arm64 libgvpr2 arm64 2.42.2-7+b3 [177 kB] Get: 166 http://deb.debian.org/debian bookworm/main arm64 liblab-gamut1 arm64 2.42.2-7+b3 [198 kB] Get: 167 http://deb.debian.org/debian bookworm/main arm64 libxmu6 arm64 2:1.1.3-3 [57.2 kB] Get: 168 http://deb.debian.org/debian bookworm/main arm64 libxaw7 arm64 2:1.0.14-1 [184 kB] Get: 169 http://deb.debian.org/debian bookworm/main arm64 graphviz arm64 2.42.2-7+b3 [567 kB] Get: 170 http://deb.debian.org/debian bookworm/main arm64 libnl-3-200 arm64 3.7.0-0.2+b1 [60.2 kB] Get: 171 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-200 arm64 3.7.0-0.2+b1 [168 kB] Get: 172 http://deb.debian.org/debian bookworm/main arm64 libibverbs1 arm64 44.0-2 [56.8 kB] Get: 173 http://deb.debian.org/debian bookworm/main arm64 ibverbs-providers arm64 44.0-2 [306 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 175 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 176 http://deb.debian.org/debian bookworm/main arm64 libblas-dev arm64 3.11.0-2 [97.6 kB] Get: 177 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-21 [9508 kB] Get: 178 http://deb.debian.org/debian bookworm/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 179 http://deb.debian.org/debian bookworm/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 180 http://deb.debian.org/debian bookworm/main arm64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 181 http://deb.debian.org/debian bookworm/main arm64 libevent-2.1-7 arm64 2.1.12-stable-8 [168 kB] Get: 182 http://deb.debian.org/debian bookworm/main arm64 libevent-core-2.1-7 arm64 2.1.12-stable-8 [124 kB] Get: 183 http://deb.debian.org/debian bookworm/main arm64 libevent-extra-2.1-7 arm64 2.1.12-stable-8 [101 kB] Get: 184 http://deb.debian.org/debian bookworm/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-8 [53.7 kB] Get: 185 http://deb.debian.org/debian bookworm/main arm64 libevent-openssl-2.1-7 arm64 2.1.12-stable-8 [59.7 kB] Get: 186 http://deb.debian.org/debian bookworm/main arm64 libevent-dev arm64 2.1.12-stable-8 [302 kB] Get: 187 http://deb.debian.org/debian bookworm/main arm64 librdmacm1 arm64 44.0-2 [64.9 kB] Get: 188 http://deb.debian.org/debian bookworm/main arm64 libfabric1 arm64 1.17.0-3 [476 kB] Get: 189 http://deb.debian.org/debian bookworm/main arm64 libfftw3-double3 arm64 3.3.10-1 [326 kB] Get: 190 http://deb.debian.org/debian bookworm/main arm64 libfftw3-long3 arm64 3.3.10-1 [529 kB] Get: 191 http://deb.debian.org/debian bookworm/main arm64 libfftw3-single3 arm64 3.3.10-1 [494 kB] Get: 192 http://deb.debian.org/debian bookworm/main arm64 libfftw3-bin arm64 3.3.10-1 [42.9 kB] Get: 193 http://deb.debian.org/debian bookworm/main arm64 libfftw3-dev arm64 3.3.10-1 [1186 kB] Get: 194 http://deb.debian.org/debian bookworm/main arm64 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 195 http://deb.debian.org/debian bookworm/main arm64 libhwloc15 arm64 2.9.0-1 [133 kB] Get: 196 http://deb.debian.org/debian bookworm/main arm64 libnuma-dev arm64 2.0.16-1 [36.0 kB] Get: 197 http://deb.debian.org/debian bookworm/main arm64 libltdl-dev arm64 2.4.7-5 [165 kB] Get: 198 http://deb.debian.org/debian bookworm/main arm64 libhwloc-dev arm64 2.9.0-1 [734 kB] Get: 199 http://deb.debian.org/debian bookworm/main arm64 libpciaccess0 arm64 0.17-2 [50.4 kB] Get: 200 http://deb.debian.org/debian bookworm/main arm64 libxnvctrl0 arm64 525.85.05-3~deb12u1 [13.4 kB] Get: 201 http://deb.debian.org/debian bookworm/main arm64 ocl-icd-libopencl1 arm64 2.3.1-1 [42.1 kB] Get: 202 http://deb.debian.org/debian bookworm/main arm64 libhwloc-plugins arm64 2.9.0-1 [17.2 kB] Get: 203 http://deb.debian.org/debian bookworm/main arm64 libnl-3-dev arm64 3.7.0-0.2+b1 [104 kB] Get: 204 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-dev arm64 3.7.0-0.2+b1 [200 kB] Get: 205 http://deb.debian.org/debian bookworm/main arm64 libibverbs-dev arm64 44.0-2 [613 kB] Get: 206 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 207 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 208 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 209 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 210 http://deb.debian.org/debian bookworm/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 211 http://deb.debian.org/debian bookworm/main arm64 libkpathsea6 arm64 2022.20220321.62855-5.1+deb12u1 [149 kB] Get: 212 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 213 http://deb.debian.org/debian bookworm/main arm64 liblapack-dev arm64 3.11.0-2 [3065 kB] Get: 214 http://deb.debian.org/debian bookworm/main arm64 libmunge2 arm64 0.5.15-2 [18.8 kB] Get: 215 http://deb.debian.org/debian bookworm/main arm64 libmuparser2v5 arm64 2.3.3-0.1 [125 kB] Get: 216 http://deb.debian.org/debian bookworm/main arm64 libmuparser-dev arm64 2.3.3-0.1 [34.4 kB] Get: 217 http://deb.debian.org/debian bookworm/main arm64 libpmix2 arm64 4.2.2-1+deb12u1 [554 kB] Get: 218 http://deb.debian.org/debian bookworm/main arm64 libucx0 arm64 1.13.1-1 [734 kB] Get: 219 http://deb.debian.org/debian bookworm/main arm64 libopenmpi3 arm64 4.1.4-3+b1 [2161 kB] Get: 220 http://deb.debian.org/debian bookworm/main arm64 openmpi-common all 4.1.4-3 [167 kB] Get: 221 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 222 http://deb.debian.org/debian bookworm/main arm64 libpmix-dev arm64 4.2.2-1+deb12u1 [884 kB] Get: 223 http://deb.debian.org/debian bookworm/main arm64 openmpi-bin arm64 4.1.4-3+b1 [225 kB] Get: 224 http://deb.debian.org/debian bookworm/main arm64 libopenmpi-dev arm64 4.1.4-3+b1 [970 kB] Get: 225 http://deb.debian.org/debian bookworm/main arm64 libpaper-utils arm64 1.1.29 [8776 B] Get: 226 http://deb.debian.org/debian bookworm/main arm64 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 227 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 228 http://deb.debian.org/debian bookworm/main arm64 libptexenc1 arm64 2022.20220321.62855-5.1+deb12u1 [43.0 kB] Get: 229 http://deb.debian.org/debian bookworm/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5336 B] Get: 230 http://deb.debian.org/debian bookworm/main arm64 libsynctex2 arm64 2022.20220321.62855-5.1+deb12u1 [57.3 kB] Get: 231 http://deb.debian.org/debian bookworm/main arm64 libteckit0 arm64 2.5.11+ds1-1+b1 [299 kB] Get: 232 http://deb.debian.org/debian bookworm/main arm64 libtexlua53-5 arm64 2022.20220321.62855-5.1+deb12u1 [103 kB] Get: 233 http://deb.debian.org/debian bookworm/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 234 http://deb.debian.org/debian bookworm/main arm64 x11proto-dev all 2022.1-1 [599 kB] Get: 235 http://deb.debian.org/debian bookworm/main arm64 libxau-dev arm64 1:1.0.9-1 [23.2 kB] Get: 236 http://deb.debian.org/debian bookworm/main arm64 libxdmcp-dev arm64 1:1.1.2-3 [41.2 kB] Get: 237 http://deb.debian.org/debian bookworm/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 238 http://deb.debian.org/debian bookworm/main arm64 libxcb1-dev arm64 1.15-1 [182 kB] Get: 239 http://deb.debian.org/debian bookworm/main arm64 libx11-dev arm64 2:1.8.4-2+deb12u2 [818 kB] Get: 240 http://deb.debian.org/debian bookworm/main arm64 libxi6 arm64 2:1.8-1+b1 [82.3 kB] Get: 241 http://deb.debian.org/debian bookworm/main arm64 libzzip-0-13 arm64 0.13.72+dfsg.1-1.1 [58.3 kB] Get: 242 http://deb.debian.org/debian bookworm/main arm64 lsb-release all 12.0-1 [6416 B] Get: 243 http://deb.debian.org/debian bookworm/main arm64 mpi-default-bin arm64 1.14 [4752 B] Get: 244 http://deb.debian.org/debian bookworm/main arm64 mpi-default-dev arm64 1.14 [5548 B] Get: 245 http://deb.debian.org/debian bookworm/main arm64 mscgen arm64 0.20-14 [47.5 kB] Get: 246 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 247 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 248 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 249 http://deb.debian.org/debian bookworm/main arm64 tex-common all 6.18 [32.5 kB] Get: 250 http://deb.debian.org/debian bookworm/main arm64 preview-latex-style all 12.2-1 [201 kB] Get: 251 http://deb.debian.org/debian bookworm/main arm64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 252 http://deb.debian.org/debian bookworm/main arm64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 253 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 254 http://deb.debian.org/debian bookworm/main arm64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 255 http://deb.debian.org/debian bookworm/main arm64 python3-babel all 2.10.3-1 [103 kB] Get: 256 http://deb.debian.org/debian bookworm/main arm64 python3-certifi all 2022.9.24-1 [153 kB] Get: 257 http://deb.debian.org/debian bookworm/main arm64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 258 http://deb.debian.org/debian bookworm/main arm64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 259 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 260 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-3 [131 kB] Get: 261 http://deb.debian.org/debian bookworm/main arm64 python3-roman all 3.3-3 [9880 B] Get: 262 http://deb.debian.org/debian bookworm/main arm64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 263 http://deb.debian.org/debian bookworm/main arm64 python3-idna all 3.3-1 [39.4 kB] Get: 264 http://deb.debian.org/debian bookworm/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 265 http://deb.debian.org/debian bookworm/main arm64 python3-markupsafe arm64 2.1.2-1+b1 [13.3 kB] Get: 266 http://deb.debian.org/debian bookworm/main arm64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 267 http://deb.debian.org/debian bookworm/main arm64 python3-packaging all 23.0-1 [32.5 kB] Get: 268 http://deb.debian.org/debian bookworm/main arm64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 269 http://deb.debian.org/debian bookworm/main arm64 python3-six all 1.16.0-4 [17.5 kB] Get: 270 http://deb.debian.org/debian bookworm/main arm64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 271 http://deb.debian.org/debian bookworm/main arm64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 272 http://deb.debian.org/debian bookworm/main arm64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 273 http://deb.debian.org/debian bookworm/main arm64 sphinx-common all 5.3.0-4 [653 kB] Get: 274 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx all 5.3.0-4 [549 kB] Get: 275 http://deb.debian.org/debian bookworm/main arm64 rdfind arm64 1.5.0-1.1+b1 [39.2 kB] Get: 276 http://deb.debian.org/debian bookworm/main arm64 symlinks arm64 1.4-4 [10.8 kB] Get: 277 http://deb.debian.org/debian bookworm/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get: 278 http://deb.debian.org/debian bookworm/main arm64 tex-gyre all 20180621-6 [6209 kB] Get: 279 http://deb.debian.org/debian bookworm/main arm64 texlive-binaries arm64 2022.20220321.62855-5.1+deb12u1 [7544 kB] Get: 280 http://deb.debian.org/debian bookworm/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 281 http://deb.debian.org/debian bookworm/main arm64 texlive-base all 2022.20230122-3 [21.9 MB] Get: 282 http://deb.debian.org/debian bookworm/main arm64 texlive-fonts-recommended all 2022.20230122-3 [4988 kB] Get: 283 http://deb.debian.org/debian bookworm/main arm64 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 284 http://deb.debian.org/debian bookworm/main arm64 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 285 http://deb.debian.org/debian bookworm/main arm64 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 286 http://deb.debian.org/debian bookworm/main arm64 texlive-latex-extra all 2022.20230122-4 [19.2 MB] Fetched 268 MB in 2s (156 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 ... 18171 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:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (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 ... 19021 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.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:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (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 ... 19455 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.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:arm64. Preparing to unpack .../003-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.2-3_arm64.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_arm64.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_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../010-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../011-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../012-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../013-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../014-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../015-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../016-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../017-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../018-libbsd0_0.11.7-2_arm64.deb ... Unpacking libbsd0:arm64 (0.11.7-2) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../019-libedit2_3.1-20221030-2_arm64.deb ... Unpacking libedit2:arm64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:arm64. Preparing to unpack .../020-libcbor0.8_0.8.0-2+b1_arm64.deb ... Unpacking libcbor0.8:arm64 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../021-libfido2-1_1.12.0-2+b1_arm64.deb ... Unpacking libfido2-1:arm64 (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../022-openssh-client_1%3a9.2p1-2+deb12u1_arm64.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_arm64.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_arm64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../030-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../031-libxml2_2.9.14+dfsg-1.3~deb12u1_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package libarchive13:arm64. Preparing to unpack .../032-libarchive13_3.6.2-1_arm64.deb ... Unpacking libarchive13:arm64 (3.6.2-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../033-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../034-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../035-libsasl2-2_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../036-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../037-libnghttp2-14_1.52.0-1+deb12u1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.52.0-1+deb12u1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../038-libpsl5_0.21.2-1_arm64.deb ... Unpacking libpsl5:arm64 (0.21.2-1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../039-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../040-libssh2-1_1.10.0-3+b1_arm64.deb ... Unpacking libssh2-1:arm64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../041-libcurl4_7.88.1-10+deb12u4_arm64.deb ... Unpacking libcurl4:arm64 (7.88.1-10+deb12u4) ... Selecting previously unselected package libjsoncpp25:arm64. Preparing to unpack .../042-libjsoncpp25_1.9.5-4_arm64.deb ... Unpacking libjsoncpp25:arm64 (1.9.5-4) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../043-librhash0_1.4.3-3_arm64.deb ... Unpacking librhash0:arm64 (1.4.3-3) ... Selecting previously unselected package libuv1:arm64. Preparing to unpack .../044-libuv1_1.44.2-1_arm64.deb ... Unpacking libuv1:arm64 (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../045-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../046-cmake_3.25.1-1_arm64.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../047-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../048-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../049-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. 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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:arm64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up libpangoft2-1.0-0:arm64 (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:arm64 (1.50.12+ds-1) ... 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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/1451124/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bookworm I: user script /srv/workspace/pbuilder/1451124/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 arm64 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=ARM_NEON_ASIMD -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 - not 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 - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/aarch64-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/aarch64-linux-gnu/libz.so (found version "1.2.13") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- 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 - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- 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/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-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/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-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=ARM_NEON_ASIMD -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 - not 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 - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/aarch64-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/aarch64-linux-gnu/libz.so (found version "1.2.13") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- 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 - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- 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/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not 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/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-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=ARM_NEON_ASIMD -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 - not 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 - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not 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/aarch64-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/aarch64-linux-gnu/libz.so (found version "1.2.13") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- 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 - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- 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/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-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/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-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=ARM_NEON_ASIMD -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 - not 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 - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not 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/aarch64-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/aarch64-linux-gnu/libz.so (found version "1.2.13") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- 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 - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- 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/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not 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/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-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 -j12 -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 /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 /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 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 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/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend /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/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 /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.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 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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/programs /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/CMakeFiles/gmx_objlib.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/programs /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving 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/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[3]: 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[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' 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/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 make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.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 -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -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/basic' /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/basic' 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 -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -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/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -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/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -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/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 -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 -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 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -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/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 -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 -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]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/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/basic/src/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 -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 -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]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' 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/c++ -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/basic/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 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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 -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 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -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/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 -isystem 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/build/reproducible-path/gromacs-2022.5/build/basic/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/basic/src/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 -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -MF CMakeFiles/view_objlib.dir/view/fgrid.cpp.o.d -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/view/fgrid.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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -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/p2p_protocol.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -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 CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -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/basic/src/gromacs && /usr/bin/cc -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 -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/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -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/basic/src/gromacs && /usr/bin/c++ -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/basic/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 -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/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/basic/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 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -Wno-missing-field-initializers -fexcess-precision=fast 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/widemuldiv.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -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 [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/basic/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 -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 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/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 /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -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 -fPIC -fopenmp -Wno-redundant-move -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 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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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /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 -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++ -DGMX_DOUBLE=0 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o 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/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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 -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/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 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 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/aarch64-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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/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 -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 /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 -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/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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-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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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/niceheader.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/path.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/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 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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 -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_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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/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_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 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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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/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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-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 -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/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_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 -I/build/reproducible-path/gromacs-2022.5/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_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/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_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_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_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/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_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/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_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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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_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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 -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 -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 -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 -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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_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 -Wno-missing-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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -Wno-missing-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 -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 -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 -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 -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 -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 -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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 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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 -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 -DTMPI_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 -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 -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/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 -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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 -DTMPI_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 -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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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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 -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/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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 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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 -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/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 -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/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 -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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 -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gpp_nextnb.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 -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/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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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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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/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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 /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 -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 -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/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 && /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/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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/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 -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/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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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 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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 -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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 -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/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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/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 -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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 -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/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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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/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_gpu_program_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 -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 -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/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 -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/src/gromacs && /usr/bin/c++ -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/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 -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 -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 -DTMPI_EXPORTS 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-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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/basic/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/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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 -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 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 = 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()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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 = 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 = 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 = 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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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 -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/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 -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -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 -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 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 -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 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/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 -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 = 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>:: | ^~~~~~~~~~~~~~~~~~~ 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 /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 -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/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 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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -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 -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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 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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 -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 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 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'/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -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 -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 -fopenmp -std=c++17 -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/samples/methane-water-integration.cpp cd 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'/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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2022.5/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /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-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 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-DGMX_DOUBLE=1 -I/build/reproducible-path/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/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 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 -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 make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 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-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 -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/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -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/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 -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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/buttons.cpp.o -MF CMakeFiles/view_objlib.dir/view/buttons.cpp.o.d -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/view/buttons.cpp 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -MF CMakeFiles/view_objlib.dir/view/dialogs.cpp.o.d -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/view/dialogs.cpp 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -MF CMakeFiles/view_objlib.dir/view/fgrid.cpp.o.d -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/view/fgrid.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -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/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 -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 -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/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 -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 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/filter.cpp.o -MF CMakeFiles/view_objlib.dir/view/filter.cpp.o.d -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/view/filter.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 0%] Built target mdrun_objlib 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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pullelement.cpp.o -MF CMakeFiles/modularsimulator.dir/pullelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/pullelement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/pullelement.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 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-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/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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/signallers.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 /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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-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 /build/reproducible-path/gromacs-2022.5/build/basic-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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/statepropagatordata.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 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-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/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 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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 -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 /build/reproducible-path/gromacs-2022.5/build/basic-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 -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-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 && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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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-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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/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/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o 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/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/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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/aarch64-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 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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 -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/strdb.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -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 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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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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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-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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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 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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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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 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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 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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 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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 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-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 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-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 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-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 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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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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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-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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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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-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 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-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 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-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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 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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 -Wno-missing-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 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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 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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 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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 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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 -Wno-missing-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 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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 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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 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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 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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 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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 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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 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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 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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 -Wno-missing-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 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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 -Wno-missing-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 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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 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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 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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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -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 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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 -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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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 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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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/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 -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -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 -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/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlineoptionsmodule.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/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/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_setup.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 -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 && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/gpuhaloexchange_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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/mdsetup.cpp cd 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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 -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/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/neldermead.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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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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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 -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 -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 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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 -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 && /usr/bin/c++ 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CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 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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 -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 -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 -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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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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/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/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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/pbcenums.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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/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/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/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/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/topsort.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ 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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 -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 -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=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/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/angle_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 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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 -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ 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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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_awh.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 -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/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_filter.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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_mindist.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 -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/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_order.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 -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++ -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_saltbr.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-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/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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-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 -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/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/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/topio.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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 && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/x2top.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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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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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/surfacearea.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/trajectory.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 -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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/mdlib/calcvir.cpp.o -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/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/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/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 -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 && /usr/bin/c++ -DGMX_DOUBLE=1 -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-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /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 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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 -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=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/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 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/gpuforcereduction_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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/lincs.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 -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-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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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-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 -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++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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 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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 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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 -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 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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 -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 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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 -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 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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 -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-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/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 -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 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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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 -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 -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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/basic-dp/src/gromacs && 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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/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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 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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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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-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 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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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-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 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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 -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 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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 -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 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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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 && 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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 -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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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-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 -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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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 -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_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 -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 -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-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DTMPI_EXPORTS 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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 -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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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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 -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 -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 -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 -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 -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-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 -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 -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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.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/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /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/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-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 -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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 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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 -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 /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 -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 -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -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 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>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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>:: | ^~~~~~~~~~~~~~~~~~~ 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>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 = 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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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 -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 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 -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 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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/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/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.3 /usr/lib/aarch64-linux-gnu/liblapack.so -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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]: 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]: 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]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' 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 -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 /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 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 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/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 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/usr/lib/aarch64-linux-gnu/libX11.so -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/molecules.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 -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 -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/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 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/build/reproducible-path/gromacs-2022.5/api/nblib/particlesequencer.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 -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 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/build/reproducible-path/gromacs-2022.5/api/nblib/topologyhelpers.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 -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 -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 make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 97%] Built target gmx cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS 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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/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 directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory 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/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 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/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.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,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/basic/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/basic' [ 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/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/testutils /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/conftest.cpp.o -MF CMakeFiles/testutils.dir/conftest.cpp.o.d -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/conftest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils && /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/testutils -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 -isystem 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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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/physicalnodecommunicator_mpi.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\" -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 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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' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -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/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o 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'/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 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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/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o 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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target mdrun_test_infrastructure /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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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/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.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 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 -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/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 -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.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/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 -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 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 -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/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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -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 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 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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/tests/kernelsetup.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 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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/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 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-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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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/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 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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/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 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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/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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 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-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' 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-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-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' 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF 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 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 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-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 -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 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 -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/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 -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/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -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/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-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/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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 nonbonded-fep-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 -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/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 -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/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/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= 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 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-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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 66%] 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/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/fft/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /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' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -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/basic/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 66%] Built target domdec-mpi-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' 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 /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2022.5/build/basic/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' /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' 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 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-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 66%] Built target density_fitting_applied_forces-test /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' 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/hardware/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests /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 -I/build/reproducible-path/gromacs-2022.5/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' 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 -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 [ 66%] Built target qmmm_applied_forces-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 -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -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/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 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-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 -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/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 -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 cd /build/reproducible-path/gromacs-2022.5/build/basic/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 66%] Built target listed_forces-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 -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/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 66%] Built target fft-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' 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/mdspan/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-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/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 -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/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 -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/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 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CMakeFiles/mdrunutility-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/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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/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.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 67%] Built target awh-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' 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/mdtypes/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f 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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 -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/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 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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/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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/template_mp.cpp 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/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' 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.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.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-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/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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests/helpformat.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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast 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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/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 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-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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 "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.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 71%] Built target mdlib-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' 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/pbcutil/tests /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= 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/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 -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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 [ 71%] 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/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/random/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /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' 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 -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/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 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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/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 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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/restraint/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /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' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/restraint/tests && 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-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 72%] Built target utility-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' 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 -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 -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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 -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 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 -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/basic/src/gromacs/restraint/tests && /usr/bin/c++ -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/basic/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/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 -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 CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/gammadistribution.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 -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 74%] Built target gpu_utils-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 -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/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 74%] 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/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 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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/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 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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/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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pme.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/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 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-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 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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 74%] Built target timing-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' 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 -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/neldermead.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" "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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 74%] Built target ewald-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' 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/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\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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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 -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 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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 74%] 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/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 -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/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 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-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/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 -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/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 -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 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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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 74%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/timeunitmanager.cpp /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 && 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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 -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 -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/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 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--color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /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' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -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/basic/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/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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 74%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make 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/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 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-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/basic/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/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 -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/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 -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/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 -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/src/gromacs/gmxana/tests && /usr/bin/c++ -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/basic/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -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/basic/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/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 -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/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 75%] Built target compat-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 /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-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/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' 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 -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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -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/basic/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/src/include -I/build/reproducible-path/gromacs-2022.5/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 75%] Built target mdtypes-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 -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/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 -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/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 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../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 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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/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 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'/build/reproducible-path/gromacs-2022.5/build/basic' [ 77%] Built target gmxana-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 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-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++ -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 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/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 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/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 -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 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 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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 78%] Built target topology-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make 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'/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 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'/build/reproducible-path/gromacs-2022.5/build/basic' [ 79%] Built target options-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' 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/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/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 -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/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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' 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/coordinateio/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /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' 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 -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/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 -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 cd /build/reproducible-path/gromacs-2022.5/build/basic/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 81%] Built target random-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' 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/energyanalysis/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /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' 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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/topdirs.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 -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 -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/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 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-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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 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-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 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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/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 [ 81%] Built target pdb2gmx2-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' 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 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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 -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/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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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/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 /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /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' 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 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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/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 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../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../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 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 82%] Built target energyanalysis-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 /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f 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'/build/reproducible-path/gromacs-2022.5/build/basic' [ 82%] Built target gmxpreprocess-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 -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/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 -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/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 -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/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 -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/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 -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_math.cpp:169:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 169 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ 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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 correlations-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' /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 -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 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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 -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/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 -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/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-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/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 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src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-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/simd/tests/simd4_floatingpoint.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 -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/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' [ 83%] Built target analysisdata-test-shared /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/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 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-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 -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/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-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/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../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 -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 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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o 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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 85%] Built target math-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' 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 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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/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 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Built target mdrun-modules-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 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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 -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 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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 -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/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/orires.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 -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/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 -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/basic/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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/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 -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/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 -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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 86%] Built target simd-test /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 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 -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/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp 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 -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 /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 -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/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 86%] Built target coordinateio-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 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'/build/reproducible-path/gromacs-2022.5/build/basic' [ 86%] Built target tool-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 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 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-test.dir/DependInfo.cmake --color= /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' /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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 86%] Built target mdrun-output-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 -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' [ 86%] 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' 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= 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 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-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 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 -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/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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-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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/fileioxdrserializer.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 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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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/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 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src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/xvgio.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 -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 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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 86%] 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 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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 -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 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 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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 -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 cd /build/reproducible-path/gromacs-2022.5/build/basic/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.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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-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 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/build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/replicaexchange_equivalence.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 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/build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/normalmodes.cpp /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 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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/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/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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/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-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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-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' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-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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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' 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 -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/__/__/__/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 [ 89%] Built target mdrun-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 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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 -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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-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" 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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 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-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 -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 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 -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/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 -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/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 -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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 90%] Built target selection-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 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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 -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 -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/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/virtualsites.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 -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/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 -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 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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 -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/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\" 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/usr/lib/aarch64-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-mpi-coordination-coupling-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' 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-integrator-test.dir/DependInfo.cmake --color= make[4]: Leaving directory 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../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 91%] 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' 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-setup-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-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' 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 -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-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' 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 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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/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 -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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 93%] Built target mdrun-io-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-simulator-comparison-test.dir/link.txt --verbose=1 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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 [ 93%] 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/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 -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/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 -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 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 | ^~~~ make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 93%] Built target mdrun-simulator-comparison-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 -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/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 -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/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 -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/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 -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-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.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-constraints-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' 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 -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 [ 93%] 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' 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 -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/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 -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/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.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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 -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' cd /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 [ 93%] 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' 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 -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/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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 94%] 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 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-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 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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/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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/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/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 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/usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 94%] Built target nblib-integrator-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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp 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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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/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 -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/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 -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/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-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.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 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 -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/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 -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/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 -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 [ 95%] Built target mdrun-pull-test 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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 mdrunutility-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 95%] Built target mdrunutility-mpi-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 -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/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 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-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 -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 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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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 -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 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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-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/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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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/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 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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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ 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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/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 -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 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 -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/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 -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 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 -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/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 -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 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:118:9: warning: iteration 2147483647 invokes undefined behavior [-Waggressive-loop-optimizations] 118 | for (int i = 0; i < count; ++i) | ^~~ /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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF 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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 -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 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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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 analysisdata-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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' [ 98%] Built target nblib-tests 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 /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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 (0 ms) 1: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 1: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 1: [ RUN ] NBlibTest.EndToEndListedComparison 1: [ OK ] NBlibTest.EndToEndListedComparison (1 ms) 1: [ RUN ] NBlibTest.shiftForcesAreCorrect 1: [ OK ] NBlibTest.shiftForcesAreCorrect (12 ms) 1: [----------] 8 tests from NBlibTest (15 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 (10 ms) 1: [----------] 1 test from LinearChainDataFixture (10 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. (28 ms total) 1: [ PASSED ] 44 tests. 1/81 Test #1: NbLibListedForcesTests ......................... Passed 0.05 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 0.01 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 5.324894 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/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 0.01 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 (1 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. (1 ms total) 5: [ PASSED ] 56 tests. 5/81 Test #5: NbLibSetupTests ................................ Passed 0.03 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 (11 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 (6 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 (7 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 (5 ms) 6: [----------] 4 tests from TprReaderTest (30 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 4 tests from 1 test suite ran. (37 ms total) 6: [ PASSED ] 4 tests. 6/81 Test #6: NbLibTprTests .................................. Passed 0.05 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 (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 (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 (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 (3 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 20 tests from 1 test suite ran. (3 ms total) 7: [ PASSED ] 20 tests. 7/81 Test #7: NbLibIntegrationTests .......................... Passed 0.02 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 0.01 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 (5 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 (6 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 (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 (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 (2 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 (0 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 59 tests from 5 test suites ran. (9 ms total) 9: [ PASSED ] 59 tests. 9/81 Test #9: TestUtilsUnitTests ............................. Passed 0.02 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 (1 ms) 10: [----------] 1 test from MpiSelfTest (1 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (1 ms total) 10: [ PASSED ] 1 test. 10/81 Test #10: TestUtilsMpiUnitTests .......................... Passed 0.01 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 (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 (6 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 (6 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 (0 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 (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 (0 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 (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. (10 ms total) 11: [ PASSED ] 386 tests. 11: 11: YOU HAVE 1 DISABLED TEST 11: 11/81 Test #11: UtilityUnitTests ............................... Passed 0.04 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 (2 ms) 12: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 12: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (4 ms) 12: [----------] 2 tests from PhysicalNodeCommunicatorTest (6 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 2 tests from 1 test suite ran. (6 ms total) 12: [ PASSED ] 2 tests. 12/81 Test #12: UtilityMpiUnitTests ............................ Passed 0.02 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 (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 (5 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 72 tests from 1 test suite ran. (5 ms total) 13: [ PASSED ] 72 tests. 13/81 Test #13: GmxlibTests .................................... Passed 0.02 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 (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 (0 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 (4 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (3 ms) 14: [----------] 14 tests from WithParameters/ConstraintsTest (9 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 (1 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 (0 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 (0 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 (3 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 (1 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 (0 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 (0 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 (0 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 (0 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 (0 ms) 14: [----------] 11 tests from WithParameters/EnergyOutputTest (12 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 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (2 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 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) 14: [----------] 16 tests from WithParameters/LeapFrogTest (10 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 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 14: [----------] 13 tests from WithParameters/SettleTest (3 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 155 tests from 17 test suites ran. (38 ms total) 14: [ PASSED ] 155 tests. 14/81 Test #14: MdlibUnitTest .................................. Passed 0.06 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 (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 (0 ms) 15: [----------] 1 test from biasGridTest (0 ms total) 15: 15: [----------] 1 test from BiasSharingTest 15: [ RUN ] BiasSharingTest.SharingWorks 15: [ OK ] BiasSharingTest.SharingWorks (11 ms) 15: [----------] 1 test from BiasSharingTest (11 ms total) 15: 15: [----------] 1 test from BiasFepLambdaStateTest 15: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 15: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 15: [----------] 1 test from BiasFepLambdaStateTest (1 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 (1 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 (3 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (2 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (2 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (2 ms) 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (12 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 21 tests from 8 test suites ran. (28 ms total) 15: [ PASSED ] 21 tests. 15/81 Test #15: AwhTest ........................................ Passed 0.04 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 (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 0.01 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 (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/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 -1567097441 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 (2 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 1601589239 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 (2 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 -1074029083 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 (2 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 -67108970 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 (6 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 -137937050 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 (7 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 -279447114 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 (2 ms) 17: [----------] 7 tests from QMMMTopologyPreprocessorTest (23 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 (0 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. (24 ms total) 17: [ PASSED ] 21 tests. 17/81 Test #17: QMMMAppliedForcesUnitTest ...................... Passed 0.04 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 (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 0.01 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 (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 (2 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 (2 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 (1 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 (0 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 (1 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 (1 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 (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 132 tests from 9 test suites ran. (13 ms total) 19: [ PASSED ] 132 tests. 19/81 Test #19: ListedForcesTest ............................... Passed 0.03 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 (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 0.01 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 (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 (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. (6 ms total) 21: [ PASSED ] 60 tests. 21/81 Test #21: CommandLineUnitTests ........................... Passed 0.02 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 0.01 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 (1 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 (3 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 4 tests from 1 test suite ran. (3 ms total) 23: [ PASSED ] 4 tests. 23/81 Test #23: DomDecMpiTests ................................. Passed 0.03 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 (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 (1 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 (1 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 (1 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 (1 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 (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 (1 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 (1 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 (1 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 (2 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 (2 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 (0 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 (1 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 (1 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 (2 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (1 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 (1 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 (1 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 (1 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 (1 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 (0 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 (1 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 (1 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 (1 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 (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 (0 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 (0 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 (0 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 (1 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 (1 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 (1 ms) 24: [----------] 108 tests from Pme_SplineAndSpreadTest (92 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_ (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_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_ (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_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 (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 (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 (7 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 (2 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 (3 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_ (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_ (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 (6 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 (8 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 (1 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 24: 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (15 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 407 tests from 9 test suites ran. (137 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 0.19 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 (5 ms) 25: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (6 ms) 25: [----------] 2 tests from ManyFFTTest (13 ms total) 25: 25: [----------] 1 test from FFTTest 25: [ RUN ] FFTTest.Real2DLength18_15Test 25: [ OK ] FFTTest.Real2DLength18_15Test (2 ms) 25: [----------] 1 test from FFTTest (2 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 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 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 (3 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (4 ms) 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (14 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 (0 ms) 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 25: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 15 tests from 4 test suites ran. (32 ms total) 25: [ PASSED ] 15 tests. 25/81 Test #25: FFTUnitTests ................................... Passed 0.07 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 0.04 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 (0 ms) 27: [----------] 1 test from CpuInfoTest (0 ms total) 27: 27: [----------] 4 tests from HardwareTopologyTest 27: [ RUN ] HardwareTopologyTest.Execute 27: [ OK ] HardwareTopologyTest.Execute (14 ms) 27: [ RUN ] HardwareTopologyTest.HwlocExecute 27: [ OK ] HardwareTopologyTest.HwlocExecute (11 ms) 27: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 27: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (10 ms) 27: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 27: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (9 ms) 27: [----------] 4 tests from HardwareTopologyTest (45 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 (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 (3 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 (3 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 (0 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 (1 ms) 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 27: 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 27: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 21 tests from 9 test suites ran. (59 ms total) 27: [ PASSED ] 21 tests. 27/81 Test #27: HardwareUnitTests .............................. Passed 0.08 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 (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 (15 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (15 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 28: [----------] 12 tests from DensitySimilarityTest (33 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 (1 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 (14 ms) 28: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 28: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 28: [----------] 2 tests from NelderMead (14 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. (51 ms total) 28: [ PASSED ] 301 tests. 28/81 Test #28: MathUnitTests .................................. Passed 0.07 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 (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 (0 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 0.02 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 (3 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 30: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (2 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 30: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (1 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 30: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 30: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (1 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 30: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 30: [----------] 6 tests from ThreadAffinityMultiRankTest (10 ms total) 30: 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (0 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (0 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (0 ms) 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (8 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 13 tests from 2 test suites ran. (19 ms total) 30: [ PASSED ] 13 tests. 30/81 Test #30: MdrunUtilityMpiUnitTests ....................... Passed 0.04 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 (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 0.01 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 (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 (6 ms) 32: [----------] 2 tests from CheckpointDataTest (8 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 (4 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. (13 ms total) 32: [ PASSED ] 93 tests. 32/81 Test #32: MdtypesUnitTest ................................ Passed 0.04 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 (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. (3 ms total) 33: [ PASSED ] 22 tests. 33/81 Test #33: OnlineHelpUnitTests ............................ Passed 0.02 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 (1 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 (1 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. (6 ms total) 34: [ PASSED ] 111 tests. 34/81 Test #34: OptionsUnitTests ............................... Passed 0.03 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 (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 (7 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 0.03 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 (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 0.03 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 0.02 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 (1 ms) 38: [ RUN ] SplineTableTest/0.Sinc 38: [ OK ] SplineTableTest/0.Sinc (0 ms) 38: [ RUN ] SplineTableTest/0.LJ12 38: [ OK ] SplineTableTest/0.LJ12 (13 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 (19 ms) 38: [ RUN ] SplineTableTest/0.ThreeFunctions 38: [ OK ] SplineTableTest/0.ThreeFunctions (17 ms) 38: [ RUN ] SplineTableTest/0.Simd 38: [ OK ] SplineTableTest/0.Simd (2 ms) 38: [ RUN ] SplineTableTest/0.SimdTwoFunctions 38: [ OK ] SplineTableTest/0.SimdTwoFunctions (12 ms) 38: [----------] 10 tests from SplineTableTest/0 (70 ms total) 38: 38: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 38: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 38: [ RUN ] SplineTableTest/1.Sinc 38: [ OK ] SplineTableTest/1.Sinc (0 ms) 38: [ RUN ] SplineTableTest/1.LJ12 38: [ OK ] SplineTableTest/1.LJ12 (0 ms) 38: [ RUN ] SplineTableTest/1.PmeCorrection 38: [ OK ] SplineTableTest/1.PmeCorrection (0 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 (1 ms) 38: [ RUN ] SplineTableTest/1.ThreeFunctions 38: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 38: [ RUN ] SplineTableTest/1.Simd 38: [ OK ] SplineTableTest/1.Simd (0 ms) 38: [ RUN ] SplineTableTest/1.SimdTwoFunctions 38: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 38: [----------] 10 tests from SplineTableTest/1 (8 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 20 tests from 2 test suites ran. (79 ms total) 38: [ PASSED ] 20 tests. 38/81 Test #38: TableUnitTests ................................. Passed 0.10 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 (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 0.02 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 (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 0.02 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 (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 (2 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 0.02 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 (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 0.02 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 (1 ms) 43: [ RUN ] SimdMathTest.sqrtUnsafe 43: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 43: [ RUN ] SimdMathTest.inv 43: [ OK ] SimdMathTest.inv (1 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 (1 ms) 43: [ RUN ] SimdMathTest.exp2Unsafe 43: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 43: [ RUN ] SimdMathTest.exp 43: [ OK ] SimdMathTest.exp (1 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 (0 ms) 43: [ RUN ] SimdMathTest.erfc 43: [ OK ] SimdMathTest.erfc (0 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 (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 (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 (2 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 (1 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 43: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracy 43: [ OK ] SimdMathTest.expSingleAccuracy (1 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 (0 ms) 43: [ RUN ] SimdMathTest.erfcSingleAccuracy 43: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.sinSingleAccuracy 43: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.cosSingleAccuracy 43: [ OK ] SimdMathTest.cosSingleAccuracy (0 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 (1 ms) 43: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 43: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 43: [----------] 56 tests from SimdMathTest (46 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. (48 ms total) 43: [ PASSED ] 288 tests. 43/81 Test #43: SimdUnitTests .................................. Passed 0.08 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 0.02 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 (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 (423 ms) 45: [----------] 1 test from GmxChiTest (467 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 (10 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 (4 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 (17 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 (0 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 (0 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 (0 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 (0 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 (0 ms) 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (3 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 22 tests from 4 test suites ran. (489 ms total) 45: [ PASSED ] 22 tests. 45/81 Test #45: GmxAnaTest ..................................... Passed 0.51 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 (1 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/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 -52462663 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 (188 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 -134383017 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 (135 ms) 46: [----------] 2 tests from GenionTest (324 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 (0 ms) 46: [----------] 1 test from GenRestrTest (0 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 -2013774849 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 -1220837 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 (2 ms) 46: [----------] 1 test from GromppDirectiveTest (2 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 (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/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 46: 46: Output configuration contains 10 atoms in 10 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 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 (0 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 (3 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 (0 ms) 46: [----------] 5 tests from InsertMoleculesTest (6 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 (1 ms) 46: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 46: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (7 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 (1 ms) 46: [ RUN ] GetIrTest.RejectsValueWithoutKey 46: [ OK ] GetIrTest.RejectsValueWithoutKey (7 ms) 46: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 46: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (7 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 (1 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 (1 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 (1 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 (1 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 (0 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 (1 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 (1 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 (1 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 (1 ms) 46: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 46: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (3 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 (1 ms) 46: [ RUN ] GetIrTest.RejectsImplicitSolventYes 46: [ OK ] GetIrTest.RejectsImplicitSolventYes (4 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (0 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (0 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 (1 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 (0 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 (1 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 (0 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 (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (0 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (0 ms) 46: [----------] 34 tests from GetIrTest (67 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 (3 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 (22 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 (22 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 (10 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 (95 ms) 46: [----------] 5 tests from SolvateTest (155 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 (2 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 (1 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 (1 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 (1 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 (0 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 ms) 46: [----------] 18 tests from SinglePeptideFragments/EditconfTest (23 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 90 tests from 11 test suites ran. (585 ms total) 46: [ PASSED ] 90 tests. 46/81 Test #46: GmxPreprocessTests ............................. Passed 0.61 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 (21 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 (22 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 (20 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 (19 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 (87 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 (21 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 (23 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 (22 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 (20 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 (95 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 (20 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 (22 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 (20 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 (18 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 (86 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 (21 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 (23 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 (22 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 (20 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 (96 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 (20 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 (22 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 (20 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 (18 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 (86 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 (21 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 (23 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 (22 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 (20 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 (96 ms) 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1061 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 30 tests from 1 test suite ran. (1061 ms total) 47: [ PASSED ] 30 tests. 47/81 Test #47: Pdb2gmx1Test ................................... Passed 1.07 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 (61 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 (55 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 (22 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 (21 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 (56 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 (21 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 (23 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 (21 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 (20 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 (58 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 (20 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 (22 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 (20 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 (19 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 (55 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 (21 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 (23 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 (21 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 (20 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 (58 ms) 48: [----------] 20 tests from G43a1/Pdb2gmxTest (647 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 (22 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 (25 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 (22 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 (21 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 (57 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 (23 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 (26 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 (23 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 (22 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 (60 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 (22 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 (25 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 (23 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 (21 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 (58 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 (23 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 (25 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 (23 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 (22 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 (61 ms) 48: [----------] 20 tests from G53a6/Pdb2gmxTest (616 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 40 tests from 2 test suites ran. (1263 ms total) 48: [ PASSED ] 40 tests. 48/81 Test #48: Pdb2gmx2Test ................................... Passed 1.28 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 (55 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 (36 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 (27 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 (23 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 (98 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 (26 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 (28 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 (27 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 (24 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 (109 ms) 49: [----------] 10 tests from Amber/Pdb2gmxTest (457 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 (10 ms) 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest (10 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 (23 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 (25 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 (23 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 (22 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 (92 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 (11 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 (25 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 (27 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 (25 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 (23 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 (105 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 (11 ms) 49: [----------] 12 tests from Charmm/Pdb2gmxTest (418 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 (23 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 (19 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 (23 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 (21 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 (24 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 (20 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 (23 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 (19 ms) 49: [----------] 8 tests from ChainSep/Pdb2gmxTest (177 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 (13 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 (13 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 (14 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 (13 ms) 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest (55 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 (744 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 (83 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 (1521 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 (83 ms) 49: [----------] 4 tests from Cyclic/Pdb2gmxTest (2431 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 39 tests from 6 test suites ran. (3550 ms total) 49: [ PASSED ] 39 tests. 49/81 Test #49: Pdb2gmx3Test ................................... Passed 3.57 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 (16 ms) 50: [ RUN ] AutocorrTest.EacNoNormalize 50: [ OK ] AutocorrTest.EacNoNormalize (13 ms) 50: [ RUN ] AutocorrTest.EacCos 50: [ OK ] AutocorrTest.EacCos (19 ms) 50: [ RUN ] AutocorrTest.EacVector 50: [ OK ] AutocorrTest.EacVector (32 ms) 50: [ RUN ] AutocorrTest.EacRcross 50: [ OK ] AutocorrTest.EacRcross (1 ms) 50: [ RUN ] AutocorrTest.EacP0 50: [ OK ] AutocorrTest.EacP0 (35 ms) 50: [ RUN ] AutocorrTest.EacP1 50: [ OK ] AutocorrTest.EacP1 (42 ms) 50: [ RUN ] AutocorrTest.EacP2 50: [ OK ] AutocorrTest.EacP2 (29 ms) 50: [ RUN ] AutocorrTest.EacP3 50: [ OK ] AutocorrTest.EacP3 (1 ms) 50: [ RUN ] AutocorrTest.EacP4 50: [ OK ] AutocorrTest.EacP4 (21 ms) 50: [----------] 10 tests from AutocorrTest (216 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 (0 ms) 50: [ RUN ] ExpfitTest.EffnEXP5 50: [ OK ] ExpfitTest.EffnEXP5 (2 ms) 50: [ RUN ] ExpfitTest.EffnEXP7 50: [ OK ] ExpfitTest.EffnEXP7 (2 ms) 50: [ RUN ] ExpfitTest.EffnEXP9 50: [ OK ] ExpfitTest.EffnEXP9 (17 ms) 50: [ RUN ] ExpfitTest.EffnERF 50: [ OK ] ExpfitTest.EffnERF (1 ms) 50: [ RUN ] ExpfitTest.EffnERREST 50: [ OK ] ExpfitTest.EffnERREST (1 ms) 50: [ RUN ] ExpfitTest.EffnVAC 50: [ OK ] ExpfitTest.EffnVAC (2 ms) 50: [ RUN ] ExpfitTest.EffnPRES 50: [ OK ] ExpfitTest.EffnPRES (7 ms) 50: [----------] 10 tests from ExpfitTest (35 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. (255 ms total) 50: [ PASSED ] 21 tests. 50/81 Test #50: CorrelationsTest ............................... Passed 0.27 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 (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 (1 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 (1 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 (0 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 (2 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 (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 (2 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 (0 ms total) 51: 51: [----------] 6 tests from AverageModuleTest 51: [ RUN ] AverageModuleTest.BasicTest 51: [ OK ] AverageModuleTest.BasicTest (0 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipointData 51: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 51: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 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 (2 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 (0 ms) 51: [----------] 2 tests from FrameAverageModuleTest (0 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 (0 ms) 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [----------] 2 tests from SimpleHistogramModuleTest (1 ms total) 51: 51: [----------] 3 tests from WeightedHistogramModuleTest 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 51: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 51: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 51: 51: [----------] 3 tests from BinAverageModuleTest 51: [ RUN ] BinAverageModuleTest.ComputesCorrectly 51: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 51: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 51: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 51: [----------] 3 tests from BinAverageModuleTest (1 ms total) 51: 51: [----------] 4 tests from AbstractAverageHistogramTest 51: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 51: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 51: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 51: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 51: [----------] 4 tests from AbstractAverageHistogramTest (2 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 (0 ms) 51: [----------] 3 tests from LifetimeModuleTest (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 69 tests from 14 test suites ran. (19 ms total) 51: [ PASSED ] 69 tests. 51/81 Test #51: AnalysisDataUnitTests .......................... Passed 0.03 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 (7 ms) 52: [----------] 1 test from OutputSelectorDeathTest (7 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 (4 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 (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 (8 ms) 52: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 52: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 52: [----------] 5 tests from TrajectoryFrameWriterTest (23 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 (3 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 (3 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 (3 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 (3 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 (3 ms) 52: [----------] 5 tests from SetAtomsTest (17 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 (3 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 (3 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 (2 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 (2 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 (2 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 (2 ms) 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (17 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 (2 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 (2 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 (2 ms) 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (7 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 (4 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 (4 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 (4 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 (4 ms) 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (17 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 (2 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 (1 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 (2 ms) 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (6 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 (1 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 (1 ms) 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (3 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 (1 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 (1 ms) 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (3 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 (1 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 (1 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 (1 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 (1 ms) 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput (6 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 64 tests from 19 test suites ran. (113 ms total) 52: [ PASSED ] 64 tests. 52/81 Test #52: CoordinateIOTests .............................. Passed 0.13 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 (2 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 11 tests from AngleModuleTest (17 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 (0 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 (0 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 (0 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 (0 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 (1 ms) 53: [----------] 5 tests from ClustsizeTest (4 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 (1 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 (1 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (3 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 (5 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 (4 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 (0 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 (0 ms) 53: [----------] 4 tests from ConvertTrjModuleTest (12 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 (1 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 (2 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 (1 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 (4 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 (4 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 (4 ms) 53: [----------] 6 tests from DistanceModuleTest (21 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 (1 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 (1 ms) 53: [----------] 2 tests from ExtractClusterModuleTest (2 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 (42 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 (42 ms) 53: [----------] 2 tests from FreeVolumeModuleTest (85 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 (1 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 (1 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 (1 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 (1 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 -148678 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 (13 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 -18879057 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 (12 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 2045247481 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 (12 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 -1181825 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 (12 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 -556294297 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 (12 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 1809708734 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 (11 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 -546319619 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 (12 ms) 53: [----------] 11 tests from MsdModuleTest (92 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 9 tests from PairDistanceModuleTest (12 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 (12 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 (9 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 (13 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 (7 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 (14 ms) 53: [----------] 5 tests from RdfModuleTest (57 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 (5 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 (3 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 (3 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 (4 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 (4 ms) 53: [----------] 5 tests from SasaModuleTest (22 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 (2 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 8 tests from SelectModuleTest (13 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 (0 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 53: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 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 (0 ms) 53: [ RUN ] SurfaceAreaTest.Computes100Points 53: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 53: [----------] 10 tests from SurfaceAreaTest (4 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 (1 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 (1 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 -1611976721 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 (156 ms) 53: [----------] 4 tests from TopologyInformation (160 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 4 tests from TrajectoryModuleTest (6 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. (516 ms total) 53: [ PASSED ] 96 tests. 53/81 Test #53: TrajectoryAnalysisUnitTests .................... Passed 0.53 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 (11 ms) 54: [----------] 1 test from DhdlTest (12 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 (14 ms) 54: [----------] 1 test from OriresTest (14 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 (2 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 (2 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 (2 ms) 54: [----------] 3 tests from EnergyTest (8 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 (36 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 (35 ms) 54: [----------] 2 tests from ViscosityTest (72 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 7 tests from 4 test suites ran. (108 ms total) 54: [ PASSED ] 7 tests. 54/81 Test #54: EnergyAnalysisUnitTests ........................ Passed 0.13 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 -20070921 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 = -20070921 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= 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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 (32 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 (34 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 (0 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 1876425983 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 (0 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 (0 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 -295708549 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 (162 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 -168427533 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 (171 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 -272633225 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 (263 ms) 55: [----------] 3 tests from ConvertTprTest (596 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 (0 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 (0 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 (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 (0 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 (4 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 (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 (0 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 (0 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 (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 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 (0 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 (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 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 (2 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 (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 (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 (9 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 54 tests from 6 test suites ran. (1016 ms total) 55: [ PASSED ] 54 tests. 55/81 Test #55: ToolUnitTests .................................. Passed 1.05 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 (0 ms) 56: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 56: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 56: [----------] 2 tests from FileMD5Test (0 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 (0 ms) 56: [----------] 4 tests from MrcDensityMap (0 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 (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 42 tests from 10 test suites ran. (2 ms total) 56: [ PASSED ] 42 tests. 56/81 Test #56: FileIOTests .................................... Passed 0.02 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 (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 (0 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 (8 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 57: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (15 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchBox 57: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 57: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (12 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 57: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 57: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 57: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (5 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (42 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 (5 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 57: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 57: [----------] 15 tests from NeighborhoodSearchTest (95 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 (1 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 (8 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 (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 (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 (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 (14 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 (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 (8 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 (11 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 (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 (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 (8 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 (0 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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 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 (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 57: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 57: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 57: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 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 (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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 57: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 57: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 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 (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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 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 (0 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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (5 ms) 57: [----------] 70 tests from SelectionCollectionDataTest (71 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 (2 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 (8 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 (9 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 201 tests from 11 test suites ran. (210 ms total) 57: [ PASSED ] 201 tests. 57/81 Test #57: SelectionUnitTests ............................. Passed 0.23 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 (13 ms) 58: [----------] 1 test from MdrunTest (13 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: 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 -1361092898 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: NOTE: 11 % of the run time was spent in pair search, 58: you might want to increase nstlist (this has no effect on accuracy) 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.030 0.015 199.3 58: (ns/day) (hour/ns) 58: Performance: 11.595 2.070 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 (35 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: 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 753041251 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 0.003 195.8 58: (ns/day) (hour/ns) 58: Performance: 52.082 0.461 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 (7 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: 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 -89135207 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: NOTE: 15 % of the run time was spent in pair search, 58: you might want to increase nstlist (this has no effect on accuracy) 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.022 0.011 199.0 58: (ns/day) (hour/ns) 58: Performance: 15.310 1.568 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 (20 ms) 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (64 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: 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: 0.116 0.058 199.8 58: (ns/day) (hour/ns) 58: Performance: 25.263 0.950 58: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (66 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: 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: 0.132 0.066 199.9 58: (ns/day) (hour/ns) 58: Performance: 22.167 1.083 58: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (73 ms) 58: [----------] 2 tests from Argon12/OutputFiles (140 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: 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 -236995780 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: 0.069 0.035 199.7 58: (ns/day) (hour/ns) 58: Performance: 17.447 1.376 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (44 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: 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 -67176626 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 0.034 199.7 58: (ns/day) (hour/ns) 58: Performance: 17.942 1.338 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (42 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: 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 -445390857 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: 0.066 0.033 199.7 58: (ns/day) (hour/ns) 58: Performance: 18.195 1.319 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (42 ms) 58: [----------] 3 tests from MdrunCanWrite/Trajectories (129 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: 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 1476375529 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: 0.035 0.018 199.4 58: (ns/day) (hour/ns) 58: Performance: 14.739 1.628 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (26 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: 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 -75661451 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: 0.036 0.018 199.3 58: (ns/day) (hour/ns) 58: Performance: 14.212 1.689 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (28 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: 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 217030653 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: 0.033 0.017 199.3 58: (ns/day) (hour/ns) 58: Performance: 15.540 1.544 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (25 ms) 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories (80 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 12 tests from 5 test suites ran. (459 ms total) 58: [ PASSED ] 12 tests. 58/81 Test #58: MdrunOutputTests ............................... Passed 0.48 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: 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 = 4.5099888e+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 -1216585743 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 (44 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 59: Number of degrees of freedom in T-Coupling group rest is 33.00 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 = -9.8207725e+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 -671646849 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 (107 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 (15 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 59: Number of degrees of freedom in T-Coupling group rest is 33.00 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 = -1.0954997e+04 59: Maximum force = 7.4724795e+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 -142619661 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 (12 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: 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 = 4.5099888e+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 -541857291 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 (3 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 59: Number of degrees of freedom in T-Coupling group rest is 33.00 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 931131903 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 (26 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 -429069 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (13 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: 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 -18876552 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: 0.037 0.018 199.6 59: (ns/day) (hour/ns) 59: Performance: 14.052 1.708 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: NOTE: 30 % 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: 0.046 0.023 199.7 59: (ns/day) (hour/ns) 59: Performance: 18.804 1.276 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 (60 ms) 59: [----------] 9 tests from DensityFittingTest (292 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: 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: 48 % 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: 0.007 0.004 199.0 59: (ns/day) (hour/ns) 59: Performance: 24.421 0.983 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 1698627465 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 (8 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: 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: 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: 0.007 0.004 198.8 59: (ns/day) (hour/ns) 59: Performance: 23.734 1.011 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 -562303025 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 (9 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: 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: NOTE: 44 % 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: 0.007 0.004 198.7 59: (ns/day) (hour/ns) 59: Performance: 23.038 1.042 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 -84411146 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 (9 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: 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: 39 % 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: 0.009 0.005 199.0 59: (ns/day) (hour/ns) 59: Performance: 18.189 1.319 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 2027941406 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 (16 ms) 59: [----------] 4 tests from MimicTest (43 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: 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 56603. 59: IMD: -imdwait not set, starting simulation. 59: starting mdrun 'Glycine' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to -1618102275 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: 10 % 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: 0.033 0.016 199.2 59: (ns/day) (hour/ns) 59: Performance: 31.682 0.758 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (77 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: 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 50623. 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 = 1.1977061e+03 59: Maximum force = 1.7794875e+04 on atom 9 59: Norm of force = 7.8732895e+03 59: Setting the LD random seed to -1107397284 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 (60 ms) 59: [----------] 2 tests from WithIntegrator/ImdTest (137 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 15 tests from 3 test suites ran. (504 ms total) 59: [ PASSED ] 15 tests. 59/81 Test #59: MdrunModulesTests .............................. Passed 0.53 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 1971318271 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 (10 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 -1258357377 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 (2 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 -939789717 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 (10 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 1808787247 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 (31 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 -545317257 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 (5 ms) 60: [----------] 5 tests from GromppTest (59 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: 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 2112749567 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: 0.048 0.024 199.5 60: (ns/day) (hour/ns) 60: Performance: 10.785 2.225 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: 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: 0.047 0.024 199.5 60: (ns/day) (hour/ns) 60: Performance: 10.967 2.188 60: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (102 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: 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 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 60: Setting the LD random seed to 994023095 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: 27 % 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 0.120 199.9 60: (ns/day) (hour/ns) 60: Performance: 1.439 16.679 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: 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 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: Core t (s) Wall t (s) (%) 60: Time: 0.766 0.383 200.0 60: (ns/day) (hour/ns) 60: Performance: 23.015 1.043 60: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (586 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: 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 -347102101 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: 46 % 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: 0.004 0.002 196.1 60: (ns/day) (hour/ns) 60: Performance: 138.123 0.174 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: 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: 0.001 0.000 191.3 60: (ns/day) (hour/ns) 60: Performance: 564.467 0.043 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: 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: 0.001 0.000 190.6 60: (ns/day) (hour/ns) 60: Performance: 606.000 0.040 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: 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: 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: 0.001 0.001 194.0 60: (ns/day) (hour/ns) 60: Performance: 377.881 0.064 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: 20 % 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 0.000 167.9 60: (ns/day) (hour/ns) 60: Performance: 786.091 0.031 60: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (17 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: 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 -538517543 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: 0.064 0.032 199.6 60: (ns/day) (hour/ns) 60: Performance: 8.136 2.950 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: 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: NOTE: 37 % 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: 0.009 0.004 198.2 60: (ns/day) (hour/ns) 60: Performance: 96.513 0.249 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (104 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: 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 -536920954 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 0.003 197.5 60: (ns/day) (hour/ns) 60: Performance: 88.828 0.270 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 (6 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: 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 -524625 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: 0.001 0.000 184.6 60: (ns/day) (hour/ns) 60: Performance: 645.584 0.037 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: 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: 0.004 0.002 197.5 60: (ns/day) (hour/ns) 60: Performance: 124.432 0.193 60: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (11 ms) 60: [----------] 6 tests from MdrunTerminationTest (829 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: 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: NOTE: 26 % 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: 0.014 0.007 198.9 60: (ns/day) (hour/ns) 60: Performance: 208.855 0.115 60: trr version: GMX_trn_file (single precision) 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (14 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: 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: 0.002 0.001 194.8 60: (ns/day) (hour/ns) 60: Performance: 1660.537 0.014 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (4 ms) 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (19 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: 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: 0.006 0.003 197.5 60: (ns/day) (hour/ns) 60: Performance: 452.154 0.053 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: 0.001 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 1162.327 0.021 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: NOTE: 20 % 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: 0.001 0.001 192.0 60: (ns/day) (hour/ns) 60: Performance: 1053.113 0.023 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: 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_secondpart.part0002.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 (13 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: 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: 0.003 0.001 195.7 60: (ns/day) (hour/ns) 60: Performance: 1149.150 0.021 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: 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: 0.002 0.001 194.4 60: (ns/day) (hour/ns) 60: Performance: 822.570 0.029 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: NOTE: 12 % 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 0.001 191.3 60: (ns/day) (hour/ns) 60: Performance: 932.121 0.026 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: 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_secondpart.part0002.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 (11 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: 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: 0.002 0.001 193.4 60: (ns/day) (hour/ns) 60: Performance: 1497.835 0.016 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: 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: 0.001 0.001 192.0 60: (ns/day) (hour/ns) 60: Performance: 1289.637 0.019 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: 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: 0.001 0.001 191.8 60: (ns/day) (hour/ns) 60: Performance: 1392.015 0.017 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 192.9 60: (ns/day) (hour/ns) 60: Performance: 2113.411 0.011 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: 0.001 0.001 190.7 60: (ns/day) (hour/ns) 60: Performance: 1174.466 0.020 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: 0.062 0.031 199.7 60: (ns/day) (hour/ns) 60: Performance: 25.185 0.953 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: 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_secondpart.part0002.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 (42 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: 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: 0.092 0.046 199.8 60: (ns/day) (hour/ns) 60: Performance: 31.989 0.750 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: 0.002 0.001 191.5 60: (ns/day) (hour/ns) 60: Performance: 826.321 0.029 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: 0.038 0.019 199.3 60: (ns/day) (hour/ns) 60: Performance: 40.709 0.590 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: 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_secondpart.part0002.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 (82 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: 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: 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: 0.033 0.017 199.6 60: (ns/day) (hour/ns) 60: Performance: 88.685 0.271 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: 0.002 0.001 193.7 60: (ns/day) (hour/ns) 60: Performance: 868.573 0.028 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: 0.002 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 861.688 0.028 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: 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_secondpart.part0002.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 (33 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: 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: 0.002 0.001 193.5 60: (ns/day) (hour/ns) 60: Performance: 1722.761 0.014 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: 0.043 0.021 199.7 60: (ns/day) (hour/ns) 60: Performance: 36.257 0.662 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: NOTE: 18 % 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: 0.019 0.009 199.3 60: (ns/day) (hour/ns) 60: Performance: 82.382 0.291 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: 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_secondpart.part0002.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 (44 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: 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: 0.001 0.001 192.1 60: (ns/day) (hour/ns) 60: Performance: 2076.371 0.012 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: 0.016 0.008 198.8 60: (ns/day) (hour/ns) 60: Performance: 96.070 0.250 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: 0.038 0.019 199.6 60: (ns/day) (hour/ns) 60: Performance: 40.532 0.592 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: 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_secondpart.part0002.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 (105 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: 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: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 194.1 60: (ns/day) (hour/ns) 60: Performance: 860.058 0.028 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: 0.002 0.001 190.4 60: (ns/day) (hour/ns) 60: Performance: 829.685 0.029 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: 0.002 0.001 190.8 60: (ns/day) (hour/ns) 60: Performance: 816.598 0.029 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: 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_secondpart.part0002.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 (22 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: 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: 0.004 0.002 195.4 60: (ns/day) (hour/ns) 60: Performance: 732.358 0.033 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: 0.017 0.009 198.8 60: (ns/day) (hour/ns) 60: Performance: 88.828 0.270 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: 0.051 0.026 199.5 60: (ns/day) (hour/ns) 60: Performance: 30.335 0.791 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: 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_secondpart.part0002.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 (60 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: 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: 0.095 0.047 199.7 60: (ns/day) (hour/ns) 60: Performance: 30.967 0.775 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: 0.029 0.015 199.1 60: (ns/day) (hour/ns) 60: Performance: 52.980 0.453 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: 0.142 0.071 199.9 60: (ns/day) (hour/ns) 60: Performance: 10.921 2.198 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: 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_secondpart.part0002.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 (203 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: 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: 0.005 0.002 196.2 60: (ns/day) (hour/ns) 60: Performance: 617.975 0.039 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: 0.003 0.002 194.5 60: (ns/day) (hour/ns) 60: Performance: 500.459 0.048 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: 0.002 0.001 193.5 60: (ns/day) (hour/ns) 60: Performance: 634.408 0.038 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: 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_secondpart.part0002.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 (31 ms) 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (662 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: 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: 0.015 0.008 198.1 60: (ns/day) (hour/ns) 60: Performance: 190.689 0.126 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: 0.009 0.005 197.0 60: (ns/day) (hour/ns) 60: Performance: 168.318 0.143 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: 0.002 0.001 191.3 60: (ns/day) (hour/ns) 60: Performance: 644.054 0.037 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: 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_secondpart.part0002.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 (41 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: 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: 0.006 0.003 197.4 60: (ns/day) (hour/ns) 60: Performance: 493.875 0.049 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: 0.003 0.002 195.5 60: (ns/day) (hour/ns) 60: Performance: 514.512 0.047 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: 0.003 0.002 190.1 60: (ns/day) (hour/ns) 60: Performance: 509.290 0.047 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: 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_secondpart.part0002.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 (31 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: 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: 0.009 0.005 197.6 60: (ns/day) (hour/ns) 60: Performance: 319.351 0.075 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: 0.002 0.001 192.8 60: (ns/day) (hour/ns) 60: Performance: 692.755 0.035 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: 0.002 0.001 192.5 60: (ns/day) (hour/ns) 60: Performance: 683.035 0.035 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: 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_secondpart.part0002.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 (38 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: 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: 0.004 0.002 195.1 60: (ns/day) (hour/ns) 60: Performance: 750.560 0.032 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: 0.002 0.001 192.6 60: (ns/day) (hour/ns) 60: Performance: 669.298 0.036 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: 0.002 0.001 191.9 60: (ns/day) (hour/ns) 60: Performance: 687.643 0.035 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: 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_secondpart.part0002.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 (31 ms) 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (143 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: 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: 0.001 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 2278.326 0.011 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: 0.001 0.000 188.0 60: (ns/day) (hour/ns) 60: Performance: 1589.420 0.015 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: 0.001 0.001 189.0 60: (ns/day) (hour/ns) 60: Performance: 1529.063 0.016 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 190.7 60: (ns/day) (hour/ns) 60: Performance: 2320.374 0.010 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: 0.001 0.001 184.3 60: (ns/day) (hour/ns) 60: Performance: 1434.884 0.017 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: 0.001 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 1429.851 0.017 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 2226.452 0.011 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: 0.001 0.001 188.5 60: (ns/day) (hour/ns) 60: Performance: 1452.780 0.017 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: 0.001 0.001 188.7 60: (ns/day) (hour/ns) 60: Performance: 1393.204 0.017 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: 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_secondpart.part0002.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 (23 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: 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: 0.002 0.001 194.1 60: (ns/day) (hour/ns) 60: Performance: 1675.896 0.014 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: 0.001 0.001 192.4 60: (ns/day) (hour/ns) 60: Performance: 1075.335 0.022 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: 0.001 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 1001.379 0.024 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: 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_secondpart.part0002.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 (13 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: 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: 0.002 0.001 194.1 60: (ns/day) (hour/ns) 60: Performance: 1714.610 0.014 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: 0.001 0.001 192.9 60: (ns/day) (hour/ns) 60: Performance: 1087.889 0.022 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: 0.001 0.001 188.3 60: (ns/day) (hour/ns) 60: Performance: 1021.130 0.024 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: 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_secondpart.part0002.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 (11 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: 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: 0.002 0.001 194.8 60: (ns/day) (hour/ns) 60: Performance: 1522.638 0.016 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: 0.002 0.001 193.6 60: (ns/day) (hour/ns) 60: Performance: 952.260 0.025 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: 0.002 0.001 188.4 60: (ns/day) (hour/ns) 60: Performance: 929.200 0.026 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: 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_secondpart.part0002.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 (12 ms) 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (81 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: 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: 0.001 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 2178.428 0.011 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: 0.001 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 1460.587 0.016 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: 0.001 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 1409.460 0.017 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: 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_secondpart.part0002.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 (12 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: 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: 0.001 0.001 190.8 60: (ns/day) (hour/ns) 60: Performance: 2203.360 0.011 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: 0.048 0.024 199.7 60: (ns/day) (hour/ns) 60: Performance: 32.033 0.749 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: Core t (s) Wall t (s) (%) 60: Time: 0.001 0.001 188.3 60: (ns/day) (hour/ns) 60: Performance: 1356.693 0.018 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: 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_secondpart.part0002.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 (36 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: 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: 0.002 0.001 194.8 60: (ns/day) (hour/ns) 60: Performance: 1515.521 0.016 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: NOTE: 21 % 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: 0.016 0.008 199.2 60: (ns/day) (hour/ns) 60: Performance: 99.396 0.241 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: 0.002 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 964.367 0.025 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: 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_secondpart.part0002.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 (20 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: 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: 0.002 0.001 194.7 60: (ns/day) (hour/ns) 60: Performance: 1684.603 0.014 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: 0.001 0.001 193.1 60: (ns/day) (hour/ns) 60: Performance: 1098.885 0.022 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: 0.001 0.001 189.0 60: (ns/day) (hour/ns) 60: Performance: 1012.571 0.024 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: 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_secondpart.part0002.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 (10 ms) 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (79 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: 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: 0.001 0.001 189.8 60: (ns/day) (hour/ns) 60: Performance: 2163.130 0.011 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: 0.001 0.000 187.7 60: (ns/day) (hour/ns) 60: Performance: 1556.055 0.015 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: 0.001 0.001 189.1 60: (ns/day) (hour/ns) 60: Performance: 1468.479 0.016 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.1 60: (ns/day) (hour/ns) 60: Performance: 2133.170 0.011 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: 0.001 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 1429.225 0.017 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: 0.049 0.025 199.7 60: (ns/day) (hour/ns) 60: Performance: 31.654 0.758 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: 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_secondpart.part0002.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 (34 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: 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: 0.055 0.028 199.7 60: (ns/day) (hour/ns) 60: Performance: 53.113 0.452 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: 0.057 0.029 199.3 60: (ns/day) (hour/ns) 60: Performance: 27.151 0.884 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 0.002 186.2 60: (ns/day) (hour/ns) 60: Performance: 494.240 0.049 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: 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_secondpart.part0002.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 (74 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: 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: 0.003 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 831.951 0.029 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: 0.002 0.001 179.2 60: (ns/day) (hour/ns) 60: Performance: 691.140 0.035 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: 0.002 0.001 188.3 60: (ns/day) (hour/ns) 60: Performance: 681.607 0.035 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: 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_secondpart.part0002.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 (25 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: 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: 0.002 0.001 186.9 60: (ns/day) (hour/ns) 60: Performance: 1159.969 0.021 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: 0.002 0.001 186.9 60: (ns/day) (hour/ns) 60: Performance: 886.034 0.027 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: 0.002 0.001 189.8 60: (ns/day) (hour/ns) 60: Performance: 730.784 0.033 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: 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_secondpart.part0002.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 (19 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: 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 0.002 194.2 60: (ns/day) (hour/ns) 60: Performance: 652.951 0.037 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: 0.002 0.001 189.7 60: (ns/day) (hour/ns) 60: Performance: 741.922 0.032 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: 0.002 0.001 190.2 60: (ns/day) (hour/ns) 60: Performance: 652.168 0.037 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: 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_secondpart.part0002.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 (19 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: 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 0.002 193.8 60: (ns/day) (hour/ns) 60: Performance: 740.990 0.032 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: 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: 0.001 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 1037.370 0.023 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: 0.002 0.001 186.1 60: (ns/day) (hour/ns) 60: Performance: 856.259 0.028 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: 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_secondpart.part0002.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 (18 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: 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: 0.001 0.001 190.0 60: (ns/day) (hour/ns) 60: Performance: 1953.883 0.012 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: 0.001 0.001 187.8 60: (ns/day) (hour/ns) 60: Performance: 1338.871 0.018 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: 0.001 0.001 188.6 60: (ns/day) (hour/ns) 60: Performance: 1174.043 0.020 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: 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_secondpart.part0002.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 (16 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: 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: 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: 0.002 0.001 191.3 60: (ns/day) (hour/ns) 60: Performance: 1632.810 0.015 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: 0.001 0.001 188.6 60: (ns/day) (hour/ns) 60: Performance: 1121.172 0.021 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: 0.001 0.001 189.3 60: (ns/day) (hour/ns) 60: Performance: 1059.958 0.023 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: 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_secondpart.part0002.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 (17 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: 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: 0.002 0.001 193.9 60: (ns/day) (hour/ns) 60: Performance: 1434.698 0.017 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: 0.002 0.001 192.7 60: (ns/day) (hour/ns) 60: Performance: 778.213 0.031 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: 0.002 0.001 186.8 60: (ns/day) (hour/ns) 60: Performance: 660.354 0.036 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: 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_secondpart.part0002.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 (17 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: 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: 0.002 0.001 193.8 60: (ns/day) (hour/ns) 60: Performance: 1492.030 0.016 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: 0.002 0.001 192.2 60: (ns/day) (hour/ns) 60: Performance: 852.232 0.028 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: 0.002 0.001 186.8 60: (ns/day) (hour/ns) 60: Performance: 926.034 0.026 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: 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_secondpart.part0002.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 (17 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: 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: 0.002 0.001 177.6 60: (ns/day) (hour/ns) 60: Performance: 1351.007 0.018 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: 0.002 0.001 192.4 60: (ns/day) (hour/ns) 60: Performance: 753.405 0.032 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: 0.002 0.001 186.2 60: (ns/day) (hour/ns) 60: Performance: 911.285 0.026 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: 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_secondpart.part0002.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 (16 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: 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: 0.136 0.068 199.9 60: (ns/day) (hour/ns) 60: Performance: 21.562 1.113 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: 0.041 0.021 199.6 60: (ns/day) (hour/ns) 60: Performance: 37.426 0.641 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: 0.002 0.001 187.4 60: (ns/day) (hour/ns) 60: Performance: 911.795 0.026 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: 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_secondpart.part0002.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 (102 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: 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: 0.002 0.001 193.3 60: (ns/day) (hour/ns) 60: Performance: 1516.641 0.016 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: 0.001 0.001 191.3 60: (ns/day) (hour/ns) 60: Performance: 1010.688 0.024 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: 0.002 0.001 187.5 60: (ns/day) (hour/ns) 60: Performance: 957.572 0.025 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: 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_secondpart.part0002.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 (10 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: 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: 0.002 0.001 194.2 60: (ns/day) (hour/ns) 60: Performance: 1565.589 0.015 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: 0.002 0.001 193.4 60: (ns/day) (hour/ns) 60: Performance: 800.955 0.030 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: 0.002 0.001 179.5 60: (ns/day) (hour/ns) 60: Performance: 808.901 0.030 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: 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_secondpart.part0002.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 (11 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: 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: 0.002 0.001 194.5 60: (ns/day) (hour/ns) 60: Performance: 1198.559 0.020 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: 0.002 0.001 191.2 60: (ns/day) (hour/ns) 60: Performance: 828.420 0.029 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: 0.004 0.002 192.6 60: (ns/day) (hour/ns) 60: Performance: 401.513 0.060 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: 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_secondpart.part0002.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 (16 ms) 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (429 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: 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: 0.076 0.038 199.6 60: (ns/day) (hour/ns) 60: Performance: 38.798 0.619 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: 0.004 0.002 193.9 60: (ns/day) (hour/ns) 60: Performance: 360.944 0.066 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: 0.004 0.002 189.9 60: (ns/day) (hour/ns) 60: Performance: 339.068 0.071 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: 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_secondpart.part0002.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 (57 ms) 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (57 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: 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: 0.003 0.002 189.7 60: (ns/day) (hour/ns) 60: Performance: 935.124 0.026 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: 0.002 0.001 186.2 60: (ns/day) (hour/ns) 60: Performance: 677.924 0.035 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: 0.002 0.001 187.0 60: (ns/day) (hour/ns) 60: Performance: 703.362 0.034 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: 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_secondpart.part0002.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 (25 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: 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: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 194.7 60: (ns/day) (hour/ns) 60: Performance: 865.617 0.028 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: 0.003 0.001 193.8 60: (ns/day) (hour/ns) 60: Performance: 551.953 0.043 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: 0.003 0.001 189.8 60: (ns/day) (hour/ns) 60: Performance: 567.314 0.042 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: 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_secondpart.part0002.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 (23 ms) 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (48 ms total) 60: 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: Setting the AWH bias MC random seed to 1954021070 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 -201326642 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: 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: 0.120 0.060 199.8 60: (ns/day) (hour/ns) 60: Performance: 24.499 0.980 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: 0.002 0.001 188.5 60: (ns/day) (hour/ns) 60: Performance: 680.044 0.035 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: 0.002 0.001 188.6 60: (ns/day) (hour/ns) 60: Performance: 652.559 0.037 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: 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_secondpart.part0002.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 (109 ms) 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: Setting the AWH bias MC random seed to 532406190 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 -486607011 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: 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: 0.004 0.002 193.3 60: (ns/day) (hour/ns) 60: Performance: 668.322 0.036 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: 0.002 0.001 189.3 60: (ns/day) (hour/ns) 60: Performance: 608.487 0.039 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: 0.002 0.001 189.5 60: (ns/day) (hour/ns) 60: Performance: 595.054 0.040 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: 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_secondpart.part0002.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 (28 ms) 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (138 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: 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: 0.016 0.008 198.9 60: (ns/day) (hour/ns) 60: Performance: 177.171 0.135 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: 0.077 0.039 199.7 60: (ns/day) (hour/ns) 60: Performance: 20.095 1.194 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: 0.005 0.003 191.2 60: (ns/day) (hour/ns) 60: Performance: 290.375 0.083 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: 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_secondpart.part0002.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 (99 ms) 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (99 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: 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 -1210123273 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: 0.001 0.000 183.0 60: (ns/day) (hour/ns) 60: Performance: 364.942 0.066 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 (5 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: 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 980279023 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 0.001 193.5 60: (ns/day) (hour/ns) 60: Performance: 172.279 0.139 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 (4 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: 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 -698788115 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: 0.001 0.000 184.4 60: (ns/day) (hour/ns) 60: Performance: 389.874 0.062 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 (4 ms) 60: [----------] 3 tests from Checking/InitialConstraintsTest (14 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 66 tests from 13 test suites ran. (2781 ms total) 60: [ PASSED ] 66 tests. 60/81 Test #60: MdrunIOTests ................................... Passed 2.79 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: 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 1874837079 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: 41 % 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: 0.285 0.143 199.9 61: (ns/day) (hour/ns) 61: Performance: 9.085 2.642 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: 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: 0.246 0.123 199.9 61: (ns/day) (hour/ns) 61: Performance: 10.533 2.279 61: [ OK ] CompelTest.SwapCanRun (520 ms) 61: [----------] 1 test from CompelTest (520 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: 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: 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: 0.000 0.000 186.9 61: (ns/day) (hour/ns) 61: Performance: 526.727 0.046 61: Setting the LD random seed to -139133003 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 (3 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: 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: 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: 0.000 0.000 186.7 61: (ns/day) (hour/ns) 61: Performance: 549.073 0.044 61: Setting the LD random seed to -167903299 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 (4 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: 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: 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: 0.000 0.000 186.1 61: (ns/day) (hour/ns) 61: Performance: 560.972 0.043 61: Setting the LD random seed to -306193442 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 (4 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: 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: 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: 0.000 0.000 185.2 61: (ns/day) (hour/ns) 61: Performance: 594.078 0.040 61: Setting the LD random seed to 468451163 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 (3 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: 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: 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: 0.000 0.000 185.8 61: (ns/day) (hour/ns) 61: Performance: 585.441 0.041 61: Setting the LD random seed to -278403585 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 (3 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: 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: 0.000 0.000 185.7 61: (ns/day) (hour/ns) 61: Performance: 590.208 0.041 61: Setting the LD random seed to 174026743 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 (4 ms) 61: [----------] 6 tests from BondedInteractionsTest (23 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: 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 -12733701 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: 0.95 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 0.002 195.4 61: (ns/day) (hour/ns) 61: Performance: 207.720 0.116 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: 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 -1078984985 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: 0.95 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 0.002 194.0 61: (ns/day) (hour/ns) 61: Performance: 258.001 0.093 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (23179 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: 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 -139264037 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: 0.95 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 29 % of the run time was spent in domain decomposition, 61: 6 % 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: 0.027 0.013 199.3 61: (ns/day) (hour/ns) 61: Performance: 32.439 0.740 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: 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 -1680998529 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: 0.95 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: 0.086 0.043 199.7 61: (ns/day) (hour/ns) 61: Performance: 10.077 2.382 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (96 ms) 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (23275 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: 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 -269287691 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: NOTE: 11 % 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: 0.031 0.016 198.8 61: (ns/day) (hour/ns) 61: Performance: 27.585 0.870 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: 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 1040176027 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: NOTE: 13 % 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 0.022 199.4 61: (ns/day) (hour/ns) 61: Performance: 19.532 1.229 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (63 ms) 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (63 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: 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: 0.113 0.057 199.8 61: (ns/day) (hour/ns) 61: Performance: 13.713 1.750 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (84 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: 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: 0.086 0.043 199.7 61: (ns/day) (hour/ns) 61: Performance: 18.114 1.325 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (56 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: 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: 0.040 0.020 199.6 61: (ns/day) (hour/ns) 61: Performance: 39.232 0.612 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (33 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: 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: 0.010 0.005 198.1 61: (ns/day) (hour/ns) 61: Performance: 158.156 0.152 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (14 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: 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: 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: 0.020 0.010 199.0 61: (ns/day) (hour/ns) 61: Performance: 79.149 0.303 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (25 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: 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: 0.104 0.052 199.8 61: (ns/day) (hour/ns) 61: Performance: 14.997 1.600 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (71 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: 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: 0.043 0.021 199.5 61: (ns/day) (hour/ns) 61: Performance: 36.488 0.658 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (40 ms) 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest (327 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: 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 -337641601 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: 0.005 0.002 196.0 61: (ns/day) (hour/ns) 61: Performance: 662.568 0.036 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (6 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: 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 -604275209 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: 0.005 0.002 196.1 61: (ns/day) (hour/ns) 61: Performance: 671.227 0.036 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (6 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: 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 1035956433 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: 0.059 0.030 199.7 61: (ns/day) (hour/ns) 61: Performance: 52.407 0.458 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: 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 1861081471 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: 0.001 0.001 188.6 61: (ns/day) (hour/ns) 61: Performance: 2872.295 0.008 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (4 ms) 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (53 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 22 tests from 6 test suites ran. (24311 ms total) 61: [ PASSED ] 21 tests. 61: [ SKIPPED ] 1 test, listed below: 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61/81 Test #61: MdrunTestsOneRank .............................. Passed 24.33 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: 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 -1094052230 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: 29.0%. 62: The balanceable part of the MD step is 17%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 5.1%. 62: 62: NOTE: 5.1 % 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: 26 % of the run time was spent in domain decomposition, 62: 19 % 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: 0.710 0.178 399.8 62: (ns/day) (hour/ns) 62: Performance: 7.300 3.288 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: Core t (s) Wall t (s) (%) 62: Time: 0.547 0.137 399.7 62: (ns/day) (hour/ns) 62: Performance: 9.477 2.533 62: [ OK ] CompelTest.SwapCanRun (620 ms) 62: [----------] 1 test from CompelTest (620 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: 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: 38 % of the run time was spent in domain decomposition, 62: 28 % 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: 0.032 0.008 398.9 62: (ns/day) (hour/ns) 62: Performance: 10.816 2.219 62: Setting the LD random seed to -1076109829 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 (34 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: 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: 33 % of the run time was spent in domain decomposition, 62: 28 % 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: 0.032 0.008 398.9 62: (ns/day) (hour/ns) 62: Performance: 10.637 2.256 62: Setting the LD random seed to 1024687103 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 (15 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: 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: 33 % of the run time was spent in domain decomposition, 62: 27 % 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: 0.033 0.008 398.9 62: (ns/day) (hour/ns) 62: Performance: 10.400 2.308 62: Setting the LD random seed to 1876926399 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 (17 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: 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: 37 % of the run time was spent in domain decomposition, 62: 29 % 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: 0.031 0.008 398.9 62: (ns/day) (hour/ns) 62: Performance: 11.020 2.178 62: Setting the LD random seed to -553992746 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 (16 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: 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: 33 % of the run time was spent in domain decomposition, 62: 28 % 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: 0.033 0.008 398.9 62: (ns/day) (hour/ns) 62: Performance: 10.427 2.302 62: Setting the LD random seed to -2935001 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 (90 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: 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: 18 % of the run time was spent in domain decomposition, 62: 15 % 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: 0.060 0.015 399.4 62: (ns/day) (hour/ns) 62: Performance: 5.789 4.146 62: Setting the LD random seed to -72682185 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 (34 ms) 62: [----------] 6 tests from BondedInteractionsTest (208 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: 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 2027944919 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: 0.95 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: 0.249 0.062 399.5 62: (ns/day) (hour/ns) 62: Performance: 6.921 3.468 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: 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 -209716483 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: 0.95 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: 0.209 0.052 399.4 62: (ns/day) (hour/ns) 62: Performance: 8.241 2.912 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (23970 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: 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 1305853851 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: 0.95 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: 0.246 0.062 399.5 62: (ns/day) (hour/ns) 62: Performance: 7.018 3.420 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: 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 1331682043 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: 0.95 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: 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: Core t (s) Wall t (s) (%) 62: Time: 0.213 0.053 399.4 62: (ns/day) (hour/ns) 62: Performance: 8.111 2.959 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (314 ms) 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (24284 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: 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 -1291976710 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: 11 % of the run time was spent in domain decomposition, 62: 8 % 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: 0.117 0.029 398.9 62: (ns/day) (hour/ns) 62: Performance: 14.727 1.630 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: 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 -1342442545 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: 10 % 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: Core t (s) Wall t (s) (%) 62: Time: 0.129 0.032 399.0 62: (ns/day) (hour/ns) 62: Performance: 13.406 1.790 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (89 ms) 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (89 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: 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: 10.3%. 62: The balanceable part of the MD step is 50%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 5.2%. 62: 62: NOTE: 5.2 % 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: Core t (s) Wall t (s) (%) 62: Time: 0.291 0.073 398.6 62: (ns/day) (hour/ns) 62: Performance: 10.647 2.254 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (95 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: 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: 10.0%. 62: The balanceable part of the MD step is 66%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 6.6%. 62: 62: NOTE: 6.6 % 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: 14 % 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: Core t (s) Wall t (s) (%) 62: Time: 0.240 0.060 397.0 62: (ns/day) (hour/ns) 62: Performance: 12.885 1.863 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (84 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: 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: 7.5%. 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: 5.1%. 62: 62: NOTE: 5.1 % 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: 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: Core t (s) Wall t (s) (%) 62: Time: 0.299 0.075 399.6 62: (ns/day) (hour/ns) 62: Performance: 10.382 2.312 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (93 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: 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: Core t (s) Wall t (s) (%) 62: Time: 0.276 0.069 399.5 62: (ns/day) (hour/ns) 62: Performance: 11.245 2.134 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (89 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: 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: Core t (s) Wall t (s) (%) 62: Time: 0.265 0.066 399.5 62: (ns/day) (hour/ns) 62: Performance: 11.740 2.044 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (84 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: 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: 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: 0.027 0.007 393.2 62: (ns/day) (hour/ns) 62: Performance: 111.573 0.215 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (32 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: 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: Core t (s) Wall t (s) (%) 62: Time: 0.229 0.058 398.7 62: (ns/day) (hour/ns) 62: Performance: 13.523 1.775 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (77 ms) 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest (557 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: 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 2110763738 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: 0.7%. 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: 0.3%. 62: 62: 62: NOTE: 42 % 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 0.002 387.3 62: (ns/day) (hour/ns) 62: Performance: 702.642 0.034 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (7 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: 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 -1115730140 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: 7.5%. 62: The balanceable part of the MD step is 69%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 5.2%. 62: 62: NOTE: 5.2 % 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: 14 % of the run time was spent in domain decomposition, 62: 8 % 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: 0.223 0.056 399.5 62: (ns/day) (hour/ns) 62: Performance: 27.858 0.862 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (71 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: 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 2080331669 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: 0.0%. 62: The balanceable part of the MD step is 75%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.0%. 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: Core t (s) Wall t (s) (%) 62: Time: 0.223 0.056 399.5 62: (ns/day) (hour/ns) 62: Performance: 27.855 0.862 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (67 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: 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 1577056063 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: 0.0%. 62: The balanceable part of the MD step is 75%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.0%. 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: Core t (s) Wall t (s) (%) 62: Time: 0.223 0.056 399.5 62: (ns/day) (hour/ns) 62: Performance: 27.834 0.862 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (67 ms) 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (213 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 22 tests from 6 test suites ran. (26017 ms total) 62: [ PASSED ] 21 tests. 62: [ SKIPPED ] 1 test, listed below: 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62/81 Test #62: MdrunTestsTwoRanks ............................. Passed 26.03 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: 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 -289810 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: 0.010 0.005 197.4 63: (ns/day) (hour/ns) 63: Performance: 379.283 0.063 63: [ OK ] OriresTest.OriresCanRun (108 ms) 63: [----------] 1 test from OriresTest (108 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: 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 562028489 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: NOTE: 12 % of the run time was spent in domain decomposition, 63: 4 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.044 0.022 199.5 63: (ns/day) (hour/ns) 63: Performance: 207.228 0.116 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 (39943 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: 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 -270832409 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: 0.010 0.005 198.3 63: (ns/day) (hour/ns) 63: Performance: 909.260 0.026 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 (16607 ms) 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (56550 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 4 tests from 2 test suites ran. (56673 ms total) 63: [ PASSED ] 4 tests. 63/81 Test #63: MdrunSingleRankAlgorithmsTests ................. Passed 56.69 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 0.112 0.1122 10.6106 5.6135 64: [ OK ] NonbondedBenchTest.BasicEndToEndTest (14 ms) 64: [----------] 1 test from NonbondedBenchTest (14 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: 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 = -4.7990997e+01 64: Maximum force = 1.8629692e+02 on atom 13 64: Norm of force = 8.7721836e+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 (151 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: 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 = -5.5862354e+01 64: Maximum force = 4.2726685e+02 on atom 13 64: Norm of force = 1.8452681e+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 (144 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: 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 = 3.1937723e+02 64: Maximum force = 9.9988691e+03 on atom 9 64: Norm of force = 4.6167015e+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 (52 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: 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 = 1.5174414e+02 64: Maximum force = 7.4208760e+03 on atom 9 64: Norm of force = 3.5692977e+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 (53 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: 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 = -1.5698468e+02 64: Maximum force = 4.5702216e+02 on atom 17 64: Norm of force = 1.8327095e+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 (12 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: 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 = 1.06799e+03 on atom 28 64: F-Norm = 4.26914e+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 = -1.6941241e+02 64: Maximum force = 2.1836787e+02 on atom 17 64: Norm of force = 7.9232440e+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 (15 ms) 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (430 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: 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 (4 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: 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 (4 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: 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: 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 = 3.1939673e+02 64: Maximum force = 9.9704229e+03 on atom 9 64: Norm of force = 4.6227534e+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 (75 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: 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 = 7.5018237e+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 (78 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: 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 = 5.6111578e+02 64: Maximum force = 1.2685402e+04 on atom 10 64: Norm of force = 6.0643536e+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 (108 ms) 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (284 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: 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: 0.001 0.001 190.5 64: (ns/day) (hour/ns) 64: Performance: 2038.582 0.012 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: 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 0.000 191.4 64: (ns/day) (hour/ns) 64: Performance: 5198.813 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.002 0.001 194.8 64: (ns/day) (hour/ns) 64: Performance: 1606.413 0.015 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: 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 0.000 192.0 64: (ns/day) (hour/ns) 64: Performance: 5212.008 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.001 0.001 191.8 64: (ns/day) (hour/ns) 64: Performance: 2198.642 0.011 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: 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 0.000 191.2 64: (ns/day) (hour/ns) 64: Performance: 5041.402 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (5 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: 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: 0.001 0.001 191.4 64: (ns/day) (hour/ns) 64: Performance: 2272.443 0.011 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: 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 0.000 192.1 64: (ns/day) (hour/ns) 64: Performance: 5404.030 0.004 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (5 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: 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: 0.001 0.001 190.4 64: (ns/day) (hour/ns) 64: Performance: 1939.123 0.012 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: 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 0.000 191.6 64: (ns/day) (hour/ns) 64: Performance: 5000.482 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (143 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: 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: 0.002 0.001 194.5 64: (ns/day) (hour/ns) 64: Performance: 1448.188 0.017 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: 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: 0.001 0.000 191.3 64: (ns/day) (hour/ns) 64: Performance: 4968.221 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (141 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: 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: 0.001 0.001 190.4 64: (ns/day) (hour/ns) 64: Performance: 2153.301 0.011 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: 19 % 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 0.000 191.6 64: (ns/day) (hour/ns) 64: Performance: 4563.403 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (141 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: 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: 0.002 0.001 192.1 64: (ns/day) (hour/ns) 64: Performance: 1653.407 0.015 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: 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 0.000 192.1 64: (ns/day) (hour/ns) 64: Performance: 4618.136 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (143 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: 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: 0.003 0.002 194.6 64: (ns/day) (hour/ns) 64: Performance: 819.555 0.029 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: 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 0.001 193.7 64: (ns/day) (hour/ns) 64: Performance: 2785.079 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 195.1 64: (ns/day) (hour/ns) 64: Performance: 768.633 0.031 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: 20 % 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: 2619.300 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 846.235 0.028 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: NOTE: 20 % 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: 2467.198 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 196.4 64: (ns/day) (hour/ns) 64: Performance: 644.481 0.037 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: 19 % 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 0.001 192.7 64: (ns/day) (hour/ns) 64: Performance: 2429.256 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 ms) 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (658 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: 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: 0.003 0.002 193.9 64: (ns/day) (hour/ns) 64: Performance: 905.437 0.027 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: 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: 0.001 0.001 193.3 64: (ns/day) (hour/ns) 64: Performance: 2171.517 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.7 64: (ns/day) (hour/ns) 64: Performance: 930.322 0.026 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: 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 0.001 192.8 64: (ns/day) (hour/ns) 64: Performance: 2187.711 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.9 64: (ns/day) (hour/ns) 64: Performance: 934.556 0.026 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: 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: 0.001 0.001 192.4 64: (ns/day) (hour/ns) 64: Performance: 2091.172 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.7 64: (ns/day) (hour/ns) 64: Performance: 912.951 0.026 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: 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 0.001 193.2 64: (ns/day) (hour/ns) 64: Performance: 2106.186 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.8 64: (ns/day) (hour/ns) 64: Performance: 922.245 0.026 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: 0.001 0.001 193.0 64: (ns/day) (hour/ns) 64: Performance: 2208.890 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.2 64: (ns/day) (hour/ns) 64: Performance: 924.459 0.026 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: 0.001 0.001 192.7 64: (ns/day) (hour/ns) 64: Performance: 2186.934 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.9 64: (ns/day) (hour/ns) 64: Performance: 950.562 0.025 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: 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: 0.001 0.001 193.6 64: (ns/day) (hour/ns) 64: Performance: 2198.642 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.6 64: (ns/day) (hour/ns) 64: Performance: 936.830 0.026 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: 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: 0.001 0.001 191.9 64: (ns/day) (hour/ns) 64: Performance: 1987.930 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.7 64: (ns/day) (hour/ns) 64: Performance: 933.848 0.026 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: 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: 0.001 0.001 193.0 64: (ns/day) (hour/ns) 64: Performance: 2198.642 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.9 64: (ns/day) (hour/ns) 64: Performance: 938.114 0.026 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: 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: 0.001 0.001 193.5 64: (ns/day) (hour/ns) 64: Performance: 2195.507 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 193.4 64: (ns/day) (hour/ns) 64: Performance: 923.212 0.026 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: 0.001 0.001 192.8 64: (ns/day) (hour/ns) 64: Performance: 2163.890 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.7 64: (ns/day) (hour/ns) 64: Performance: 716.431 0.033 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: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 1053.453 0.023 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (13 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: 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: 0.004 0.002 196.7 64: (ns/day) (hour/ns) 64: Performance: 724.605 0.033 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: 0.001 0.001 193.2 64: (ns/day) (hour/ns) 64: Performance: 2183.059 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.8 64: (ns/day) (hour/ns) 64: Performance: 713.941 0.034 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: 0.001 0.001 193.2 64: (ns/day) (hour/ns) 64: Performance: 2207.307 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.8 64: (ns/day) (hour/ns) 64: Performance: 730.707 0.033 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: 0.001 0.001 193.5 64: (ns/day) (hour/ns) 64: Performance: 2232.908 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.6 64: (ns/day) (hour/ns) 64: Performance: 702.222 0.034 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: 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 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 2216.041 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.7 64: (ns/day) (hour/ns) 64: Performance: 729.582 0.033 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: 0.001 0.001 192.3 64: (ns/day) (hour/ns) 64: Performance: 2109.792 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.7 64: (ns/day) (hour/ns) 64: Performance: 725.373 0.033 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: 0.001 0.001 193.5 64: (ns/day) (hour/ns) 64: Performance: 2216.838 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.7 64: (ns/day) (hour/ns) 64: Performance: 739.567 0.032 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: 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: 0.001 0.001 192.9 64: (ns/day) (hour/ns) 64: Performance: 2136.128 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 740.723 0.032 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: 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: 0.001 0.001 193.1 64: (ns/day) (hour/ns) 64: Performance: 2145.054 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.8 64: (ns/day) (hour/ns) 64: Performance: 736.913 0.033 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: 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: 0.001 0.001 193.2 64: (ns/day) (hour/ns) 64: Performance: 2212.857 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 196.5 64: (ns/day) (hour/ns) 64: Performance: 733.055 0.033 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: 0.001 0.001 193.0 64: (ns/day) (hour/ns) 64: Performance: 2208.890 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 194.9 64: (ns/day) (hour/ns) 64: Performance: 816.730 0.029 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: 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: 0.001 0.001 193.1 64: (ns/day) (hour/ns) 64: Performance: 1987.930 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 837.379 0.029 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: 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: 0.001 0.001 192.6 64: (ns/day) (hour/ns) 64: Performance: 1952.645 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.004 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 781.405 0.031 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: 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: 0.001 0.001 192.5 64: (ns/day) (hour/ns) 64: Performance: 2019.205 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 194.9 64: (ns/day) (hour/ns) 64: Performance: 839.890 0.029 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: 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: 0.001 0.001 192.2 64: (ns/day) (hour/ns) 64: Performance: 2043.315 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 194.9 64: (ns/day) (hour/ns) 64: Performance: 854.570 0.028 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: 0.001 0.001 193.2 64: (ns/day) (hour/ns) 64: Performance: 1907.305 0.013 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (19 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: 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: 0.003 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 823.719 0.029 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: 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: 0.001 0.001 192.9 64: (ns/day) (hour/ns) 64: Performance: 2039.932 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 194.6 64: (ns/day) (hour/ns) 64: Performance: 842.878 0.028 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: 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: 0.001 0.001 191.9 64: (ns/day) (hour/ns) 64: Performance: 1973.917 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 194.9 64: (ns/day) (hour/ns) 64: Performance: 840.692 0.029 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: 0.001 0.001 191.9 64: (ns/day) (hour/ns) 64: Performance: 1955.123 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 839.089 0.029 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: 0.001 0.001 192.5 64: (ns/day) (hour/ns) 64: Performance: 2053.531 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 856.590 0.028 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: 0.001 0.001 193.5 64: (ns/day) (hour/ns) 64: Performance: 2047.389 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 841.496 0.029 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: 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: 0.001 0.001 192.8 64: (ns/day) (hour/ns) 64: Performance: 2040.607 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 ms) 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (480 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 58 tests from 5 test suites ran. (1899 ms total) 64: [ PASSED ] 58 tests. 64/81 Test #64: MdrunNonIntegratorTests ........................ Passed 1.92 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: 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 (193 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: 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 (140 ms) 65: [----------] 2 tests from Simple/TpiTest (334 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 2 tests from 1 test suite ran. (349 ms total) 65: [ PASSED ] 2 tests. 65/81 Test #65: MdrunTpiTests .................................. Passed 0.37 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: 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: 25 % 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: 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: 0.001 0.000 279.6 66: (ns/day) (hour/ns) 66: Performance: 294.744 0.081 66: Setting the LD random seed to -1670381665 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 (10 ms) 66: [----------] 1 test from DomainDecompositionSpecialCasesTest (10 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: 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: 17 % of the run time was spent in domain decomposition, 66: 8 % 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 0.000 375.4 66: (ns/day) (hour/ns) 66: Performance: 206.607 0.116 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 -59119781 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 (9 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: 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: 19 % of the run time was spent in domain decomposition, 66: 9 % 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 0.000 375.9 66: (ns/day) (hour/ns) 66: Performance: 209.291 0.115 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 2145806332 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 (9 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: 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: 18 % 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 0.000 373.8 66: (ns/day) (hour/ns) 66: Performance: 207.020 0.116 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 -394403 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 (8 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: 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: 14 % of the run time was spent in domain decomposition, 66: 8 % 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 0.001 383.9 66: (ns/day) (hour/ns) 66: Performance: 147.103 0.163 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 -473063426 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 (21 ms) 66: [----------] 4 tests from MimicTest (49 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: 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 = -4.7990952e+01 66: Maximum force = 1.8629709e+02 on atom 13 66: Norm of force = 8.7721970e+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 (169 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: 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 = -5.5862228e+01 66: Maximum force = 4.2727219e+02 on atom 13 66: Norm of force = 1.8452919e+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 (144 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: 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 = 3.1937720e+02 66: Maximum force = 9.9988691e+03 on atom 9 66: Norm of force = 4.6167015e+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 (57 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: 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 = 1.5174358e+02 66: Maximum force = 7.4208833e+03 on atom 9 66: Norm of force = 3.5692986e+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 (54 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: 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 = -1.5698456e+02 66: Maximum force = 4.5702222e+02 on atom 17 66: Norm of force = 1.8327095e+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 (9 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: 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 = 1.06799e+03 on atom 28 66: F-Norm = 4.26914e+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 = -1.6941235e+02 66: Maximum force = 2.1838167e+02 on atom 17 66: Norm of force = 7.9235200e+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 (10 ms) 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (445 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: 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 (4 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: 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 (4 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 (2 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: 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 = 3.1939664e+02 66: Maximum force = 9.9704229e+03 on atom 9 66: Norm of force = 4.6227537e+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 (54 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: 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 = 1.5625764e+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 (53 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 (50 ms) 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (169 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 17 tests from 4 test suites ran. (723 ms total) 66: [ PASSED ] 17 tests. 66/81 Test #66: MdrunMpiTests .................................. Passed 0.74 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. (14 ms total) 67: [ PASSED ] 2 tests. 67: 67: YOU HAVE 4 DISABLED TESTS 67: 67/81 Test #67: MdrunMultiSimTests ............................. Passed 0.03 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. (8 ms total) 68: [ PASSED ] 1 test. 68: 68: YOU HAVE 4 DISABLED TESTS 68: 68/81 Test #68: MdrunMultiSimReplexTests ....................... Passed 0.02 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 0.02 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 1474920446 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 -1513134786 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: 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: 0.030 0.015 199.5 70: (ns/day) (hour/ns) 70: Performance: 119.547 0.201 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 (9726 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 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: 0.028 0.014 199.4 70: (ns/day) (hour/ns) 70: Performance: 128.511 0.187 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 (18 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: 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: 0.002 0.001 191.7 70: (ns/day) (hour/ns) 70: Performance: 66.505 0.361 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 (29871 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: 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: 0.029 0.014 199.4 70: (ns/day) (hour/ns) 70: Performance: 126.242 0.190 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 (19 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 (39637 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 19 tests from 1 test suite ran. (39654 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 39.67 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 -151111681 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 -889589923 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: 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: 13.5%. 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: 1.1%. 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: 0.044 0.011 398.3 71: (ns/day) (hour/ns) 71: Performance: 163.886 0.146 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 (9701 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 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: 15.7%. 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: 1.3%. 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.042 0.011 398.3 71: (ns/day) (hour/ns) 71: Performance: 171.668 0.140 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 (20 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: 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: 0.007 0.002 382.2 71: (ns/day) (hour/ns) 71: Performance: 47.318 0.507 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 (30706 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: 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: 4.510 1.128 400.0 71: (ns/day) (hour/ns) 71: Performance: 1.609 14.915 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 (6623 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 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: 1.249 0.312 399.9 71: (ns/day) (hour/ns) 71: Performance: 5.808 4.132 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 (479 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: 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: 0.015 0.004 394.2 71: (ns/day) (hour/ns) 71: Performance: 22.864 1.050 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 (20172 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: 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: 9.6%. 71: The balanceable part of the MD step is 7%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.7%. 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.037 0.009 398.2 71: (ns/day) (hour/ns) 71: Performance: 194.877 0.123 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 (18 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 (67723 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 19 tests from 1 test suite ran. (67747 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 67.77 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: 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 97.9 72: (ns/day) (hour/ns) 72: Performance: 957.060 0.025 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: 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 95.8 72: (ns/day) (hour/ns) 72: Performance: 2312.535 0.010 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: 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: 0.000 0.001 95.2 72: (ns/day) (hour/ns) 72: Performance: 2845.540 0.008 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: 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 95.4 72: (ns/day) (hour/ns) 72: Performance: 2641.764 0.009 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: 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 95.4 72: (ns/day) (hour/ns) 72: Performance: 2658.867 0.009 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: 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 95.4 72: (ns/day) (hour/ns) 72: Performance: 2788.861 0.009 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 (23 ms) 72: [----------] 1 test from BasicPropagators/PeriodicActionsTest (23 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 1 test from 1 test suite ran. (30 ms total) 72: [ PASSED ] 1 test. 72/81 Test #72: MdrunMpiCoordinationBasicTestsOneRank .......... Passed 0.04 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: 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: 0.7%. 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: 0.4%. 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: 0.006 0.003 195.6 73: (ns/day) (hour/ns) 73: Performance: 448.729 0.053 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: 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 62%, 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: 24 % 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 0.002 190.4 73: (ns/day) (hour/ns) 73: Performance: 953.210 0.025 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: 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: 2.8%. 73: The balanceable part of the MD step is 57%, 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: 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: 0.003 0.001 189.7 73: (ns/day) (hour/ns) 73: Performance: 1005.319 0.024 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: 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: 0.6%. 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: 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: 0.003 0.001 189.3 73: (ns/day) (hour/ns) 73: Performance: 1091.626 0.022 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: 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: 2.4%. 73: The balanceable part of the MD step is 57%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 1.4%. 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: 0.003 0.002 169.6 73: (ns/day) (hour/ns) 73: Performance: 800.441 0.030 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: 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: 4.7%. 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: 2.6%. 73: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 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 0.002 193.4 73: (ns/day) (hour/ns) 73: Performance: 757.062 0.032 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 (60 ms) 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest (60 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (76 ms total) 73: [ PASSED ] 1 test. 73/81 Test #73: MdrunMpiCoordinationBasicTestsTwoRanks ......... Passed 0.09 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: 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 95.7 74: (ns/day) (hour/ns) 74: Performance: 680.653 0.035 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 1724.208 0.014 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: 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 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2278.326 0.011 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: 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 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2158.582 0.011 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: 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 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2303.887 0.010 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: 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 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2377.690 0.010 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 (36 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: 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: 0.001 0.001 96.0 74: (ns/day) (hour/ns) 74: Performance: 1569.978 0.015 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: 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: 0.001 0.001 95.4 74: (ns/day) (hour/ns) 74: Performance: 2333.558 0.010 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2655.428 0.009 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2376.772 0.010 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2481.109 0.010 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2576.576 0.009 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 (28 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 1945.246 0.012 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: 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: 0.001 0.001 95.5 74: (ns/day) (hour/ns) 74: Performance: 2330.028 0.010 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: 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: 0.000 0.001 94.4 74: (ns/day) (hour/ns) 74: Performance: 2872.072 0.008 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2749.038 0.009 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2689.041 0.009 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2696.102 0.009 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 (24 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: 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 95.8 74: (ns/day) (hour/ns) 74: Performance: 2222.436 0.011 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: 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 95.4 74: (ns/day) (hour/ns) 74: Performance: 2631.608 0.009 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: 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: 0.000 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2884.173 0.008 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: 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 95.1 74: (ns/day) (hour/ns) 74: Performance: 2689.041 0.009 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: 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 94.6 74: (ns/day) (hour/ns) 74: Performance: 2684.355 0.009 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: 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: 0.000 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2923.870 0.008 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 (23 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 2138.353 0.011 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2603.801 0.009 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: 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: 0.000 0.000 94.6 74: (ns/day) (hour/ns) 74: Performance: 2996.398 0.008 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2713.918 0.009 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2702.015 0.009 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2731.971 0.009 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 (23 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: 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: 0.001 0.001 95.8 74: (ns/day) (hour/ns) 74: Performance: 2087.629 0.011 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: 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: 0.001 0.001 95.3 74: (ns/day) (hour/ns) 74: Performance: 2624.880 0.009 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: 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: 0.000 0.000 94.8 74: (ns/day) (hour/ns) 74: Performance: 2953.305 0.008 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2728.341 0.009 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2757.652 0.009 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: 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: 0.000 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2819.494 0.009 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 (23 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: 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: 0.001 0.001 95.8 74: (ns/day) (hour/ns) 74: Performance: 2163.890 0.011 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2641.764 0.009 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: 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: 0.000 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2900.468 0.008 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2696.102 0.009 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2767.562 0.009 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2712.723 0.009 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 (23 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: 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 0.001 95.8 74: (ns/day) (hour/ns) 74: Performance: 2238.588 0.011 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: 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 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2715.114 0.009 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: 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: 0.000 0.000 94.6 74: (ns/day) (hour/ns) 74: Performance: 3088.017 0.008 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: 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: 0.000 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2844.226 0.008 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: 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: 0.000 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2885.524 0.008 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: 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: 0.000 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2886.876 0.008 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 (23 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: 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: 0.001 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 2190.823 0.011 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: 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: 0.001 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2653.141 0.009 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: 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: 0.000 0.000 94.6 74: (ns/day) (hour/ns) 74: Performance: 2987.679 0.008 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2706.763 0.009 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: 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: 0.000 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2828.555 0.008 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: 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: 0.001 0.001 94.5 74: (ns/day) (hour/ns) 74: Performance: 2740.478 0.009 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 (23 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 2161.612 0.011 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2640.632 0.009 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: 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: 0.000 0.000 94.4 74: (ns/day) (hour/ns) 74: Performance: 2987.679 0.008 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2683.185 0.009 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: 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: 0.001 0.001 94.5 74: (ns/day) (hour/ns) 74: Performance: 2736.825 0.009 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: 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: 0.000 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2800.270 0.009 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 (23 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: 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 0.001 95.6 74: (ns/day) (hour/ns) 74: Performance: 2208.890 0.011 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2634.984 0.009 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: 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: 0.000 0.000 94.5 74: (ns/day) (hour/ns) 74: Performance: 3031.788 0.008 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: 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: 0.000 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2791.388 0.009 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: 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: 0.000 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2788.861 0.009 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: 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 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2781.306 0.009 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 (23 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: 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: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 2139.095 0.011 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 2613.744 0.009 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: 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: 0.000 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 2907.312 0.008 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: 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: 0.001 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 2767.562 0.009 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: 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: 0.001 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 2786.338 0.009 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 2721.110 0.009 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 (22 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: 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 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 2015.901 0.012 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: 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 96.9 74: (ns/day) (hour/ns) 74: Performance: 694.464 0.035 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 1248.347 0.019 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: 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 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 1159.314 0.021 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: 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 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 1174.341 0.020 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 1244.564 0.019 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 (49 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: 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: 866.103 0.028 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: 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 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1055.981 0.023 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: 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 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1172.553 0.020 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: 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 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 1131.007 0.021 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 1921.583 0.012 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: 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 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 1961.348 0.012 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 (43 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: 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: 0.001 0.001 97.6 74: (ns/day) (hour/ns) 74: Performance: 1324.005 0.018 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1508.840 0.016 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1794.522 0.013 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: 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: 0.001 0.001 97.1 74: (ns/day) (hour/ns) 74: Performance: 1785.679 0.013 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1747.686 0.014 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: 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: 0.001 0.001 97.4 74: (ns/day) (hour/ns) 74: Performance: 1797.664 0.013 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 (30 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: 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: 0.001 0.001 98.0 74: (ns/day) (hour/ns) 74: Performance: 1078.158 0.022 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1743.729 0.014 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: 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: 0.001 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1923.382 0.012 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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1779.490 0.013 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1766.225 0.014 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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1698.537 0.014 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 (28 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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1637.585 0.015 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1847.254 0.013 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 2055.587 0.012 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 2005.402 0.012 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1977.084 0.012 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: 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 1919.786 0.013 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 (25 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: 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: 0.001 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1606.413 0.015 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: 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: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 1845.594 0.013 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1982.811 0.012 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1766.732 0.014 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: 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 1808.747 0.013 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1793.999 0.013 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 (26 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: 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: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 1567.182 0.015 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1766.225 0.014 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: 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 2011.951 0.012 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: 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 1832.419 0.013 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: 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 1903.768 0.013 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1868.545 0.013 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 (26 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1389.085 0.017 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: 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: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 1544.008 0.016 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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1629.356 0.015 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: 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: 0.002 0.002 97.5 74: (ns/day) (hour/ns) 74: Performance: 634.328 0.038 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: 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: 0.002 0.002 97.4 74: (ns/day) (hour/ns) 74: Performance: 650.744 0.037 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: 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: 0.002 0.002 97.4 74: (ns/day) (hour/ns) 74: Performance: 666.947 0.036 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 (41 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: 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 97.7 74: (ns/day) (hour/ns) 74: Performance: 403.920 0.059 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: 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 97.6 74: (ns/day) (hour/ns) 74: Performance: 491.511 0.049 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: 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: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 698.559 0.034 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: 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 97.8 74: (ns/day) (hour/ns) 74: Performance: 556.915 0.043 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: 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: 0.002 0.002 97.3 74: (ns/day) (hour/ns) 74: Performance: 649.304 0.037 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: 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: 0.002 0.002 97.0 74: (ns/day) (hour/ns) 74: Performance: 851.146 0.028 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 (56 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: 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: 0.001 0.001 97.3 74: (ns/day) (hour/ns) 74: Performance: 1036.265 0.023 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1155.834 0.021 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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1361.457 0.018 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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1057.431 0.023 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1356.063 0.018 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: 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: 0.001 0.001 97.1 74: (ns/day) (hour/ns) 74: Performance: 1415.903 0.017 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 (35 ms) 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (664 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 22 tests from 1 test suite ran. (677 ms total) 74: [ PASSED ] 22 tests. 74/81 Test #74: MdrunMpiCoordinationCouplingTestsOneRank ....... Passed 0.70 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: 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: 0.4%. 75: The balanceable part of the MD step is 46%, 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: 13 % of the run time was spent in domain decomposition, 75: 2 % 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: 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: 0.006 0.003 195.6 75: (ns/day) (hour/ns) 75: Performance: 445.403 0.054 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: 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: 3.2%. 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: 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 0.001 190.6 75: (ns/day) (hour/ns) 75: Performance: 1004.663 0.024 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: 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: 7.1%. 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: 3.8%. 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: 0.003 0.002 192.2 75: (ns/day) (hour/ns) 75: Performance: 935.053 0.026 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: 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: 11.1%. 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: 5.5%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.5 % 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: 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: 0.002 0.001 190.6 75: (ns/day) (hour/ns) 75: Performance: 1256.879 0.019 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: 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: 6.3%. 75: The balanceable part of the MD step is 47%, 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: 12 % of the run time was spent in domain decomposition, 75: 4 % 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: 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: 0.002 0.001 190.8 75: (ns/day) (hour/ns) 75: Performance: 1262.675 0.019 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: 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: 14.4%. 75: The balanceable part of the MD step is 46%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 6.6%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.6 % 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: 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: 0.002 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1279.060 0.019 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 (50 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 7.6%. 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: 4.1%. 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: 0.003 0.002 193.7 75: (ns/day) (hour/ns) 75: Performance: 823.664 0.029 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 9.7%. 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: 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: 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: 0.002 0.001 191.8 75: (ns/day) (hour/ns) 75: Performance: 1178.948 0.020 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 12.0%. 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: 6.5%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.5 % 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: 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: 0.002 0.001 191.5 75: (ns/day) (hour/ns) 75: Performance: 1266.179 0.019 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 11.6%. 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: 6.3%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.3 % 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: 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: 0.002 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1354.572 0.018 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 12.5%. 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: 6.4%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.4 % 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: 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: 0.002 0.001 191.6 75: (ns/day) (hour/ns) 75: Performance: 1218.231 0.020 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 12.2%. 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: 6.4%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.4 % 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: 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: 0.002 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1336.789 0.018 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 (37 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: 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: 9.2%. 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: 5.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.2 % 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: 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: 0.003 0.001 192.6 75: (ns/day) (hour/ns) 75: Performance: 1005.319 0.024 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: 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: 9.6%. 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: 5.4%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.4 % 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: 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: 0.002 0.001 192.2 75: (ns/day) (hour/ns) 75: Performance: 1296.967 0.019 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: 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: 16.4%. 75: The balanceable part of the MD step is 43%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 7.1%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 7.1 % 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: 14 % of the run time was spent in domain decomposition, 75: 7 % 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: 0.002 0.001 191.9 75: (ns/day) (hour/ns) 75: Performance: 1143.604 0.021 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: 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: 10.1%. 75: The balanceable part of the MD step is 48%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 4.8%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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: 0.002 0.002 120.8 75: (ns/day) (hour/ns) 75: Performance: 794.403 0.030 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: 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: 11.7%. 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: 6.1%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.1 % 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: 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: 0.002 0.001 191.0 75: (ns/day) (hour/ns) 75: Performance: 1377.285 0.017 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: 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: 13.6%. 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: 7.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 7.2 % 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: 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: 0.002 0.001 191.8 75: (ns/day) (hour/ns) 75: Performance: 1140.323 0.021 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 (37 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: 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: 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: 0.002 0.001 192.4 75: (ns/day) (hour/ns) 75: Performance: 1357.258 0.018 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: 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: 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: 0.002 0.001 191.0 75: (ns/day) (hour/ns) 75: Performance: 1480.378 0.016 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: 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: 0.002 0.001 190.7 75: (ns/day) (hour/ns) 75: Performance: 1745.953 0.014 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: 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1298.060 0.018 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: 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: 0.002 0.001 190.9 75: (ns/day) (hour/ns) 75: Performance: 1418.674 0.017 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: 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: 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: 0.002 0.001 190.2 75: (ns/day) (hour/ns) 75: Performance: 1596.629 0.015 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 (33 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: 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: 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: 0.002 0.001 192.6 75: (ns/day) (hour/ns) 75: Performance: 1156.485 0.021 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: 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: 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: 0.002 0.001 191.7 75: (ns/day) (hour/ns) 75: Performance: 1365.985 0.018 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: 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: 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: 0.001 0.001 186.9 75: (ns/day) (hour/ns) 75: Performance: 2189.266 0.011 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: 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: 11 % of the run time was spent in domain decomposition, 75: 2 % 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: 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: 0.002 0.001 185.8 75: (ns/day) (hour/ns) 75: Performance: 1265.399 0.019 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: 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: 0.001 0.001 185.9 75: (ns/day) (hour/ns) 75: Performance: 1961.036 0.012 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: 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: 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: 0.002 0.001 190.4 75: (ns/day) (hour/ns) 75: Performance: 1385.337 0.017 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 (32 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: 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: 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1254.320 0.019 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: 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: 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: 0.002 0.001 190.8 75: (ns/day) (hour/ns) 75: Performance: 1385.804 0.017 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: 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: 0.002 0.001 189.9 75: (ns/day) (hour/ns) 75: Performance: 1532.486 0.016 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: 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: 0.002 0.001 190.3 75: (ns/day) (hour/ns) 75: Performance: 1335.341 0.018 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: 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: 0.002 0.001 190.2 75: (ns/day) (hour/ns) 75: Performance: 1453.313 0.017 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: 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: 0.002 0.001 182.4 75: (ns/day) (hour/ns) 75: Performance: 1267.612 0.019 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 (34 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: 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: 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1191.259 0.020 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: 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: 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: 0.002 0.001 191.6 75: (ns/day) (hour/ns) 75: Performance: 1285.197 0.019 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: 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: 0.002 0.001 190.4 75: (ns/day) (hour/ns) 75: Performance: 1597.872 0.015 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: 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: 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: 0.002 0.001 191.3 75: (ns/day) (hour/ns) 75: Performance: 1281.055 0.019 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: 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: 0.002 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1487.886 0.016 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: 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: 0.002 0.001 190.4 75: (ns/day) (hour/ns) 75: Performance: 1306.179 0.018 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 (34 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: 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: 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: 0.002 0.001 191.8 75: (ns/day) (hour/ns) 75: Performance: 1229.659 0.020 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: 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: 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: 0.002 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1419.165 0.017 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: 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: 0.002 0.001 190.4 75: (ns/day) (hour/ns) 75: Performance: 1702.057 0.014 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: 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: 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: 0.002 0.001 189.8 75: (ns/day) (hour/ns) 75: Performance: 1702.998 0.014 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: 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: 0.002 0.001 190.3 75: (ns/day) (hour/ns) 75: Performance: 1542.076 0.016 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: 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: 0.002 0.001 190.4 75: (ns/day) (hour/ns) 75: Performance: 1406.368 0.017 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 (32 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: 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: 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: 0.002 0.001 191.4 75: (ns/day) (hour/ns) 75: Performance: 1304.243 0.018 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: 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: 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: 0.002 0.001 190.8 75: (ns/day) (hour/ns) 75: Performance: 1421.785 0.017 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: 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: 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: 0.002 0.001 190.7 75: (ns/day) (hour/ns) 75: Performance: 1505.521 0.016 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: 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: 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: 0.002 0.001 189.9 75: (ns/day) (hour/ns) 75: Performance: 1412.332 0.017 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: 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: 0.002 0.001 190.3 75: (ns/day) (hour/ns) 75: Performance: 1393.642 0.017 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: 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: 0.002 0.001 189.9 75: (ns/day) (hour/ns) 75: Performance: 1597.457 0.015 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 (33 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: 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: 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1151.190 0.021 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: 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: 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: 0.002 0.001 190.8 75: (ns/day) (hour/ns) 75: Performance: 1465.761 0.016 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: 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: 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: 0.002 0.001 190.2 75: (ns/day) (hour/ns) 75: Performance: 1664.575 0.014 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: 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: 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: 0.002 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1517.575 0.016 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: 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: 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: 0.002 0.001 190.1 75: (ns/day) (hour/ns) 75: Performance: 1591.268 0.015 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: 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: 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: 0.002 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1568.379 0.015 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 (33 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: 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: 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: 0.002 0.001 191.9 75: (ns/day) (hour/ns) 75: Performance: 1304.796 0.018 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: 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: 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: 0.002 0.001 190.9 75: (ns/day) (hour/ns) 75: Performance: 1520.383 0.016 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: 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: 0.002 0.001 190.9 75: (ns/day) (hour/ns) 75: Performance: 1472.593 0.016 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: 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: 0.002 0.001 189.8 75: (ns/day) (hour/ns) 75: Performance: 1558.263 0.015 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: 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: 0.002 0.001 189.6 75: (ns/day) (hour/ns) 75: Performance: 1587.168 0.015 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: 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: 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: 0.002 0.001 190.7 75: (ns/day) (hour/ns) 75: Performance: 1513.102 0.016 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 (32 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: 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: 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: 0.002 0.001 193.1 75: (ns/day) (hour/ns) 75: Performance: 1311.602 0.018 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: 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: 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1544.396 0.016 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: 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: 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: 0.002 0.001 191.0 75: (ns/day) (hour/ns) 75: Performance: 1622.703 0.015 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: 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: 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: 0.002 0.001 191.3 75: (ns/day) (hour/ns) 75: Performance: 1737.336 0.014 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: 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: 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: 0.002 0.001 191.7 75: (ns/day) (hour/ns) 75: Performance: 1567.781 0.015 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: 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: 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: 0.002 0.001 190.8 75: (ns/day) (hour/ns) 75: Performance: 1678.636 0.014 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 (32 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: 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: 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: 0.002 0.001 193.0 75: (ns/day) (hour/ns) 75: Performance: 1260.737 0.019 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: 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: 0.002 0.001 188.4 75: (ns/day) (hour/ns) 75: Performance: 1466.808 0.016 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: 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: 0.002 0.001 191.6 75: (ns/day) (hour/ns) 75: Performance: 1589.215 0.015 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: 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: 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: 0.002 0.001 192.1 75: (ns/day) (hour/ns) 75: Performance: 1477.183 0.016 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: 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: 0.003 0.002 188.7 75: (ns/day) (hour/ns) 75: Performance: 909.850 0.026 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: 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: 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: 0.002 0.001 178.8 75: (ns/day) (hour/ns) 75: Performance: 1461.068 0.016 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 (42 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: 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: 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: 0.002 0.001 193.0 75: (ns/day) (hour/ns) 75: Performance: 1235.826 0.019 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: 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: 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: 0.002 0.001 192.2 75: (ns/day) (hour/ns) 75: Performance: 1410.715 0.017 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: 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: 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1465.587 0.016 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: 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: 0.002 0.001 190.7 75: (ns/day) (hour/ns) 75: Performance: 1609.771 0.015 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: 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: 0.002 0.001 191.4 75: (ns/day) (hour/ns) 75: Performance: 1545.558 0.016 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: 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: 0.002 0.001 191.6 75: (ns/day) (hour/ns) 75: Performance: 1511.061 0.016 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 (33 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: 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: 6.3%. 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: 3.8%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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: 0.003 0.002 192.6 75: (ns/day) (hour/ns) 75: Performance: 822.729 0.029 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: 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: 8.8%. 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: 4.8%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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: 0.003 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 878.516 0.027 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: 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: 14.2%. 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: 7.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 7.7 % 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: 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: 0.003 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 963.647 0.025 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: 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: 7.5%. 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: 4.0%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 929.620 0.026 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: 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: 14.5%. 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: 7.6%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 7.6 % 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: 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: 0.003 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1017.691 0.024 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: 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: 8.8%. 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: 4.5%. 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: 0.003 0.002 188.2 75: (ns/day) (hour/ns) 75: Performance: 867.262 0.028 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 (35 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 7.7%. 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: 4.4%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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: 0.003 0.002 192.4 75: (ns/day) (hour/ns) 75: Performance: 818.847 0.029 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 9.8%. 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: 5.0%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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 0.002 192.5 75: (ns/day) (hour/ns) 75: Performance: 798.832 0.030 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 12.1%. 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: 6.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.9 % 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: 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: 0.003 0.002 191.1 75: (ns/day) (hour/ns) 75: Performance: 917.848 0.026 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 11.5%. 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: 6.4%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.4 % 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: 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: 0.003 0.002 191.4 75: (ns/day) (hour/ns) 75: Performance: 907.371 0.026 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 11.7%. 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: 6.6%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.6 % 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: 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: 0.003 0.002 181.6 75: (ns/day) (hour/ns) 75: Performance: 876.766 0.027 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 11.4%. 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: 6.1%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.1 % 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: 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: 0.003 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 891.483 0.027 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 (37 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: 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 0.003 189.0 75: (ns/day) (hour/ns) 75: Performance: 495.324 0.048 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: 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 0.002 187.2 75: (ns/day) (hour/ns) 75: Performance: 589.643 0.041 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: 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: 0.004 0.002 185.8 75: (ns/day) (hour/ns) 75: Performance: 664.860 0.036 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: 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: 0.004 0.002 186.1 75: (ns/day) (hour/ns) 75: Performance: 624.458 0.038 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: 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: 0.004 0.002 186.4 75: (ns/day) (hour/ns) 75: Performance: 687.528 0.035 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: 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: 0.005 0.003 190.0 75: (ns/day) (hour/ns) 75: Performance: 566.961 0.042 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 (68 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: 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: 0.006 0.003 191.9 75: (ns/day) (hour/ns) 75: Performance: 493.084 0.049 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: 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: 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 0.002 188.5 75: (ns/day) (hour/ns) 75: Performance: 741.883 0.032 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: 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: 0.004 0.002 190.4 75: (ns/day) (hour/ns) 75: Performance: 696.703 0.034 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: 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: 0.004 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 666.515 0.036 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: 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: 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: 0.004 0.002 191.4 75: (ns/day) (hour/ns) 75: Performance: 671.418 0.036 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: 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: 0.003 0.002 159.9 75: (ns/day) (hour/ns) 75: Performance: 728.073 0.033 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 (50 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: 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: 0.003 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 801.065 0.030 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: 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: 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: 0.003 0.002 189.1 75: (ns/day) (hour/ns) 75: Performance: 915.393 0.026 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: 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: 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: 0.004 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 776.529 0.031 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: 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: 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: 0.003 0.002 187.8 75: (ns/day) (hour/ns) 75: Performance: 955.427 0.025 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: 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: 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: 0.003 0.001 189.4 75: (ns/day) (hour/ns) 75: Performance: 986.563 0.024 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: 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: 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: 0.003 0.002 189.5 75: (ns/day) (hour/ns) 75: Performance: 959.893 0.025 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 (37 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: 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: 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: 0.004 0.002 192.9 75: (ns/day) (hour/ns) 75: Performance: 674.468 0.036 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: 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: 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: 0.004 0.002 191.9 75: (ns/day) (hour/ns) 75: Performance: 730.707 0.033 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: 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: 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: 0.004 0.002 191.1 75: (ns/day) (hour/ns) 75: Performance: 800.025 0.030 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: 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: 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: 0.004 0.002 192.5 75: (ns/day) (hour/ns) 75: Performance: 721.550 0.033 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: 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: 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: 0.004 0.002 191.3 75: (ns/day) (hour/ns) 75: Performance: 758.414 0.032 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: 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: 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: 0.004 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 718.604 0.033 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 (38 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: 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: 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: 0.006 0.003 193.8 75: (ns/day) (hour/ns) 75: Performance: 441.430 0.054 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: 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: 20 % of the run time was 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 0.003 192.7 75: (ns/day) (hour/ns) 75: Performance: 497.103 0.048 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: 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: 20 % of the run time was 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 0.003 193.6 75: (ns/day) (hour/ns) 75: Performance: 529.534 0.045 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: 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: 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: 0.005 0.003 193.4 75: (ns/day) (hour/ns) 75: Performance: 547.122 0.044 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: 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: 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: 0.005 0.003 193.5 75: (ns/day) (hour/ns) 75: Performance: 530.217 0.045 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: 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: 20 % of the run time was 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 0.003 193.6 75: (ns/day) (hour/ns) 75: Performance: 532.210 0.045 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 (43 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: 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: 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: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 688.181 0.035 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: 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: 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: 0.004 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 737.884 0.033 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: 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: 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: 0.004 0.002 191.3 75: (ns/day) (hour/ns) 75: Performance: 765.481 0.031 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: 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: 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: 0.004 0.002 191.7 75: (ns/day) (hour/ns) 75: Performance: 717.391 0.033 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: 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: 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: 0.004 0.002 191.7 75: (ns/day) (hour/ns) 75: Performance: 708.521 0.034 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: 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: 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: 0.004 0.002 191.7 75: (ns/day) (hour/ns) 75: Performance: 745.428 0.032 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 (37 ms) 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (851 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 22 tests from 1 test suite ran. (866 ms total) 75: [ PASSED ] 22 tests. 75/81 Test #75: MdrunMpiCoordinationCouplingTestsTwoRanks ...... Passed 0.89 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: 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: 0.001 0.001 95.7 76: (ns/day) (hour/ns) 76: Performance: 1961.973 0.012 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: 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: 0.001 0.001 95.0 76: (ns/day) (hour/ns) 76: Performance: 2493.158 0.010 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: 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: 0.001 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2721.110 0.009 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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2491.142 0.010 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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2519.670 0.010 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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2543.598 0.009 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 (825 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: 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 0.001 95.5 76: (ns/day) (hour/ns) 76: Performance: 1852.810 0.013 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: 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 0.001 95.0 76: (ns/day) (hour/ns) 76: Performance: 2346.893 0.010 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: 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 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2662.314 0.009 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: 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 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2407.422 0.010 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: 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 0.001 94.8 76: (ns/day) (hour/ns) 76: Performance: 2444.680 0.010 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: 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 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2409.305 0.010 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 (768 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: 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: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 1934.252 0.012 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: 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: 0.001 0.001 94.7 76: (ns/day) (hour/ns) 76: Performance: 2322.999 0.010 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: 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: 0.001 0.001 94.1 76: (ns/day) (hour/ns) 76: Performance: 2424.476 0.010 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: 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: 0.001 0.001 94.1 76: (ns/day) (hour/ns) 76: Performance: 2510.429 0.010 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: 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: 0.001 0.001 94.1 76: (ns/day) (hour/ns) 76: Performance: 2512.477 0.010 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: 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: 0.001 0.001 94.3 76: (ns/day) (hour/ns) 76: Performance: 2532.098 0.009 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 (771 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: 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: 0.001 0.001 95.7 76: (ns/day) (hour/ns) 76: Performance: 1895.567 0.013 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: 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: 0.001 0.001 94.8 76: (ns/day) (hour/ns) 76: Performance: 2327.387 0.010 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: 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: 0.001 0.001 94.1 76: (ns/day) (hour/ns) 76: Performance: 2634.984 0.009 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: 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: 0.001 0.001 94.3 76: (ns/day) (hour/ns) 76: Performance: 2384.131 0.010 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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2510.429 0.010 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: 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: 0.001 0.001 94.1 76: (ns/day) (hour/ns) 76: Performance: 2467.198 0.010 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 (771 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: 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 0.001 95.8 76: (ns/day) (hour/ns) 76: Performance: 1860.083 0.013 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: 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 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2253.326 0.011 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: 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 0.001 94.2 76: (ns/day) (hour/ns) 76: Performance: 2470.166 0.010 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: 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 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2409.305 0.010 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: 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 0.001 93.9 76: (ns/day) (hour/ns) 76: Performance: 2408.363 0.010 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: 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 0.001 93.7 76: (ns/day) (hour/ns) 76: Performance: 2260.768 0.011 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 (774 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: 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: 0.001 0.001 96.8 76: (ns/day) (hour/ns) 76: Performance: 1803.981 0.013 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: 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: 0.001 0.001 96.2 76: (ns/day) (hour/ns) 76: Performance: 2147.297 0.011 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: 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: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 2567.984 0.009 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: 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: 0.001 0.001 95.8 76: (ns/day) (hour/ns) 76: Performance: 2353.168 0.010 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: 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: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 2288.482 0.010 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: 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: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 2315.142 0.010 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 (773 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: 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: 0.001 0.001 96.6 76: (ns/day) (hour/ns) 76: Performance: 1809.279 0.013 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: 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: 0.001 0.001 95.4 76: (ns/day) (hour/ns) 76: Performance: 2101.874 0.011 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: 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: 0.001 0.001 95.3 76: (ns/day) (hour/ns) 76: Performance: 2303.026 0.010 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: 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: 0.001 0.001 96.6 76: (ns/day) (hour/ns) 76: Performance: 1523.391 0.016 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: 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: 0.001 0.001 95.1 76: (ns/day) (hour/ns) 76: Performance: 2271.605 0.011 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: 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: 0.001 0.001 95.2 76: (ns/day) (hour/ns) 76: Performance: 2304.749 0.010 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 (772 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: 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: 0.001 0.001 97.5 76: (ns/day) (hour/ns) 76: Performance: 1483.765 0.016 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: 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: 0.001 0.001 97.3 76: (ns/day) (hour/ns) 76: Performance: 1693.401 0.014 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: 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: 0.001 0.001 96.8 76: (ns/day) (hour/ns) 76: Performance: 1860.083 0.013 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: 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 98.1 76: (ns/day) (hour/ns) 76: Performance: 957.804 0.025 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: 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: 0.001 0.001 97.8 76: (ns/day) (hour/ns) 76: Performance: 984.750 0.024 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: 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: 0.001 0.001 96.5 76: (ns/day) (hour/ns) 76: Performance: 1764.707 0.014 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 (779 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1576.406 0.015 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: 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: 0.001 0.001 96.3 76: (ns/day) (hour/ns) 76: Performance: 1722.279 0.014 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: 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: 0.001 0.001 96.4 76: (ns/day) (hour/ns) 76: Performance: 1904.945 0.013 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1824.820 0.013 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: 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: 0.001 0.001 96.5 76: (ns/day) (hour/ns) 76: Performance: 1772.323 0.014 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: 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: 0.001 0.001 96.2 76: (ns/day) (hour/ns) 76: Performance: 1788.790 0.013 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 (775 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: 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: 0.001 0.001 97.1 76: (ns/day) (hour/ns) 76: Performance: 1468.206 0.016 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: 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: 0.001 0.001 96.5 76: (ns/day) (hour/ns) 76: Performance: 1670.443 0.014 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1778.976 0.013 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: 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: 0.001 0.001 96.5 76: (ns/day) (hour/ns) 76: Performance: 1591.885 0.015 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1692.471 0.014 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: 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: 0.001 0.001 96.6 76: (ns/day) (hour/ns) 76: Performance: 1652.077 0.015 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 (778 ms) 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (7792 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 10 tests from 1 test suite ran. (7807 ms total) 76: [ PASSED ] 10 tests. 76/81 Test #76: MdrunMpiCoordinationConstraintsTestsOneRank .... Passed 7.83 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: 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 got disabled because it was unsuitable to use. 77: Average load imbalance: 12.0%. 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: 6.6%. 77: 77: NOTE: 6.6 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.002 0.001 193.7 77: (ns/day) (hour/ns) 77: Performance: 1146.477 0.021 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: 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 got disabled because it was unsuitable to use. 77: Average load imbalance: 16.1%. 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: 8.4%. 77: 77: NOTE: 8.4 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.002 0.001 193.0 77: (ns/day) (hour/ns) 77: Performance: 1302.589 0.018 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: 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 got disabled because it was unsuitable to use. 77: Average load imbalance: 20.0%. 77: The balanceable part of the MD step is 48%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 9.5%. 77: 77: NOTE: 9.5 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 13 % of the run time was spent in domain decomposition, 77: 5 % 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: 20 % 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: 0.002 0.001 193.0 77: (ns/day) (hour/ns) 77: Performance: 1403.164 0.017 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: 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 got disabled because it was unsuitable to use. 77: Average load imbalance: 16.6%. 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: 8.4%. 77: 77: NOTE: 8.4 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 10 % of the run time was spent in domain decomposition, 77: 5 % 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: 23 % 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: 0.002 0.001 190.9 77: (ns/day) (hour/ns) 77: Performance: 1204.888 0.020 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: 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 got disabled because it was unsuitable to use. 77: Average load imbalance: 20.7%. 77: The balanceable part of the MD step is 49%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 10.1%. 77: 77: NOTE: 10.1 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 10 % of the run time was spent in domain decomposition, 77: 5 % 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: 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: 0.002 0.001 192.2 77: (ns/day) (hour/ns) 77: Performance: 1391.596 0.017 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: 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 got disabled because it was unsuitable to use. 77: Average load imbalance: 21.3%. 77: The balanceable part of the MD step is 49%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 10.4%. 77: 77: NOTE: 10.4 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 10 % of the run time was spent in domain decomposition, 77: 5 % 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: 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: 0.002 0.001 192.4 77: (ns/day) (hour/ns) 77: Performance: 1393.012 0.017 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 (917 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: 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: 13.0%. 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: 7.0%. 77: 77: NOTE: 7.0 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.003 0.001 193.3 77: (ns/day) (hour/ns) 77: Performance: 1062.354 0.023 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: 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: 15.0%. 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: 8.1%. 77: 77: NOTE: 8.1 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.002 0.001 192.7 77: (ns/day) (hour/ns) 77: Performance: 1282.922 0.019 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: 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 53%, 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: 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: 0.001 0.001 188.5 77: (ns/day) (hour/ns) 77: Performance: 2018.213 0.012 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: 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: 17.9%. 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: 9.0%. 77: 77: NOTE: 9.0 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 23 % 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: 0.002 0.001 192.4 77: (ns/day) (hour/ns) 77: Performance: 1286.271 0.019 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: 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 51%, 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: 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: 0.002 0.001 188.3 77: (ns/day) (hour/ns) 77: Performance: 1807.686 0.013 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: 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: 2.3%. 77: The balanceable part of the MD step is 49%, 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: 11 % of the run time was spent in domain decomposition, 77: 4 % 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: 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: 0.001 0.001 188.1 77: (ns/day) (hour/ns) 77: Performance: 1853.925 0.013 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 (1183 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: 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: 0.002 0.001 190.7 77: (ns/day) (hour/ns) 77: Performance: 1519.633 0.016 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: 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: 0.002 0.001 189.7 77: (ns/day) (hour/ns) 77: Performance: 1840.357 0.013 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: 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: 0.001 0.001 189.1 77: (ns/day) (hour/ns) 77: Performance: 2102.592 0.011 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: 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: 0.002 0.001 188.3 77: (ns/day) (hour/ns) 77: Performance: 1803.717 0.013 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: 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: 0.001 0.001 189.3 77: (ns/day) (hour/ns) 77: Performance: 1860.925 0.013 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: 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: 0.001 0.001 188.6 77: (ns/day) (hour/ns) 77: Performance: 2020.529 0.012 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 (1369 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: 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: 0.002 0.001 190.6 77: (ns/day) (hour/ns) 77: Performance: 1531.343 0.016 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: 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: 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: 0.002 0.001 189.5 77: (ns/day) (hour/ns) 77: Performance: 1791.652 0.013 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: 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: 0.001 0.001 187.6 77: (ns/day) (hour/ns) 77: Performance: 1846.978 0.013 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: 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: 0.002 0.001 188.6 77: (ns/day) (hour/ns) 77: Performance: 1828.883 0.013 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: 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: 0.001 0.001 187.9 77: (ns/day) (hour/ns) 77: Performance: 1878.803 0.013 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: 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: 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: 0.002 0.001 188.5 77: (ns/day) (hour/ns) 77: Performance: 1680.926 0.014 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 (862 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: 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: 0.003 0.002 192.8 77: (ns/day) (hour/ns) 77: Performance: 970.401 0.025 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: 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: 0.002 0.001 189.2 77: (ns/day) (hour/ns) 77: Performance: 1796.091 0.013 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: 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: 0.001 0.001 185.1 77: (ns/day) (hour/ns) 77: Performance: 1849.473 0.013 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: 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: 11 % of the run time was spent in domain decomposition, 77: 2 % 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: 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: 0.002 0.001 185.3 77: (ns/day) (hour/ns) 77: Performance: 1587.373 0.015 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: 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: 0.001 0.001 187.8 77: (ns/day) (hour/ns) 77: Performance: 1976.133 0.012 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: 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: 0.001 0.001 188.1 77: (ns/day) (hour/ns) 77: Performance: 1942.486 0.012 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 (885 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: 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: 0.002 0.001 192.1 77: (ns/day) (hour/ns) 77: Performance: 1391.596 0.017 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: 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: 0.002 0.001 191.3 77: (ns/day) (hour/ns) 77: Performance: 1688.065 0.014 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: 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: 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: 0.002 0.001 191.1 77: (ns/day) (hour/ns) 77: Performance: 1786.456 0.013 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: 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: 0.002 0.001 189.8 77: (ns/day) (hour/ns) 77: Performance: 1798.451 0.013 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: 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: 0.002 0.001 190.4 77: (ns/day) (hour/ns) 77: Performance: 1862.895 0.013 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: 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: 0.001 0.001 190.1 77: (ns/day) (hour/ns) 77: Performance: 1897.903 0.013 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 (923 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: 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: 0.002 0.001 191.6 77: (ns/day) (hour/ns) 77: Performance: 1343.348 0.018 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: 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: 0.002 0.001 190.5 77: (ns/day) (hour/ns) 77: Performance: 1674.302 0.014 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: 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: 0.003 0.002 193.8 77: (ns/day) (hour/ns) 77: Performance: 923.281 0.026 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: 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: 0.002 0.001 190.1 77: (ns/day) (hour/ns) 77: Performance: 1751.662 0.014 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: 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: 0.002 0.001 190.1 77: (ns/day) (hour/ns) 77: Performance: 1764.455 0.014 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: 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: 0.002 0.001 190.2 77: (ns/day) (hour/ns) 77: Performance: 1702.762 0.014 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 (906 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: 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: 1.3%. 77: The balanceable part of the MD step is 64%, 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: 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: 0.003 0.001 190.6 77: (ns/day) (hour/ns) 77: Performance: 1098.537 0.022 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: 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: 1.2%. 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: 0.7%. 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: 0.002 0.001 189.1 77: (ns/day) (hour/ns) 77: Performance: 1171.327 0.020 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: 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 61%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.9%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.002 0.001 188.4 77: (ns/day) (hour/ns) 77: Performance: 1314.961 0.018 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: 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: 2.9%. 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: 1.7%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.003 0.001 190.0 77: (ns/day) (hour/ns) 77: Performance: 1045.764 0.023 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: 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: 3.2%. 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: 1.7%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.002 0.001 188.8 77: (ns/day) (hour/ns) 77: Performance: 1257.392 0.019 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: 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 59%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.1%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.002 0.001 188.6 77: (ns/day) (hour/ns) 77: Performance: 1300.389 0.018 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 (896 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: 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: 0.003 0.001 189.1 77: (ns/day) (hour/ns) 77: Performance: 1025.313 0.023 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: 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: 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: 0.002 0.001 183.5 77: (ns/day) (hour/ns) 77: Performance: 1145.411 0.021 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: 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: 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: 0.003 0.001 189.4 77: (ns/day) (hour/ns) 77: Performance: 1103.357 0.022 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: 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: 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: 0.003 0.001 187.8 77: (ns/day) (hour/ns) 77: Performance: 1074.304 0.022 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: 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: 0.002 0.001 187.9 77: (ns/day) (hour/ns) 77: Performance: 1179.400 0.020 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: 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: 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: 0.002 0.001 187.7 77: (ns/day) (hour/ns) 77: Performance: 1176.135 0.020 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 (921 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: 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: 0.003 0.002 187.7 77: (ns/day) (hour/ns) 77: Performance: 960.342 0.025 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: 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: 0.003 0.001 188.2 77: (ns/day) (hour/ns) 77: Performance: 1053.994 0.023 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: 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: 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: 0.002 0.001 187.2 77: (ns/day) (hour/ns) 77: Performance: 1209.976 0.020 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: 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: 0.003 0.001 186.8 77: (ns/day) (hour/ns) 77: Performance: 1096.191 0.022 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: 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: 0.003 0.001 187.6 77: (ns/day) (hour/ns) 77: Performance: 1090.467 0.022 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: 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: 0.003 0.001 187.1 77: (ns/day) (hour/ns) 77: Performance: 1090.274 0.022 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 (1038 ms) 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (9905 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 10 tests from 1 test suite ran. (9920 ms total) 77: [ PASSED ] 10 tests. 77/81 Test #77: MdrunMpiCoordinationConstraintsTestsTwoRanks ... Passed 9.94 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: 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 -1644183561 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: 1.053 0.527 200.0 78: (ns/day) (hour/ns) 78: Performance: 3.445 6.967 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 (10746 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: 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 -591933515 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: 0.838 0.419 200.0 78: (ns/day) (hour/ns) 78: Performance: 4.331 5.542 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 (449 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: 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 -1292206625 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: 0.649 0.325 200.0 78: (ns/day) (hour/ns) 78: Performance: 5.589 4.294 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 (355 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: 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 -33556994 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: 4.250 2.125 200.0 78: (ns/day) (hour/ns) 78: Performance: 4.107 5.844 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 (2150 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: 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 2000512637 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: 0.95 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: 1.057 0.528 200.0 78: (ns/day) (hour/ns) 78: Performance: 3.433 6.991 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 (560 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: 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 -16810003 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: 1.009 0.505 200.0 78: (ns/day) (hour/ns) 78: Performance: 3.595 6.675 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 (536 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: 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 2147349938 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: 0.89 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: 0.454 0.227 199.9 78: (ns/day) (hour/ns) 78: Performance: 7.995 3.002 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 (252 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: 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: 0.027 0.013 199.0 78: (ns/day) (hour/ns) 78: Performance: 134.455 0.178 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 2113631551 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: 0.90 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (32 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: 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 1844436815 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: 0.95 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: 0.846 0.423 200.0 78: (ns/day) (hour/ns) 78: Performance: 4.291 5.593 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 (449 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: 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 -42010369 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: 0.90 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: 0.559 0.279 200.0 78: (ns/day) (hour/ns) 78: Performance: 6.492 3.697 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 (299 ms) 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest (15832 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 10 tests from 1 test suite ran. (15839 ms total) 78: [ PASSED ] 10 tests. 78/81 Test #78: MdrunFEPTests .................................. Passed 15.85 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: 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: Core t (s) Wall t (s) (%) 79: Time: 0.944 0.472 200.0 79: (ns/day) (hour/ns) 79: Performance: 3.844 6.244 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 (855 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: 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: Core t (s) Wall t (s) (%) 79: Time: 2.440 1.220 200.0 79: (ns/day) (hour/ns) 79: Performance: 1.487 16.139 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 (1607 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: 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: 0.368 0.184 199.9 79: (ns/day) (hour/ns) 79: Performance: 9.869 2.432 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 (531 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: 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: 0.406 0.203 199.9 79: (ns/day) (hour/ns) 79: Performance: 8.927 2.689 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 (580 ms) 79: [----------] 4 tests from PullTest/PullIntegrationTest (3576 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 4 tests from 1 test suite ran. (3584 ms total) 79: [ PASSED ] 4 tests. 79/81 Test #79: MdrunPullTests ................................. Passed 3.60 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 0.04 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: 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: 1.9%. 81: The balanceable part of the MD step is 45%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.9%. 81: 81: 81: NOTE: 38 % 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 0.002 194.5 81: (ns/day) (hour/ns) 81: Performance: 473.744 0.051 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 (63 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: 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: 1.2%. 81: The balanceable part of the MD step is 40%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.5%. 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: 0.002 0.001 189.4 81: (ns/day) (hour/ns) 81: Performance: 871.474 0.028 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 (59 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: 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: 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: 0.001 0.001 188.4 81: (ns/day) (hour/ns) 81: Performance: 1075.335 0.022 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 (388 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: 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: 16 % of the run time was spent in domain decomposition, 81: 0 % 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: 13 % 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: 0.911 0.490 186.1 81: (ns/day) (hour/ns) 81: Performance: 1.588 15.109 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 (1368 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: 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: 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: 0.002 0.001 188.1 81: (ns/day) (hour/ns) 81: Performance: 946.457 0.025 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 (63 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: 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: 17 % of the run time was spent in domain decomposition, 81: 0 % 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: 11 % 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: 1.148 0.598 192.0 81: (ns/day) (hour/ns) 81: Performance: 1.300 18.456 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 (1608 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: 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: 11 % of the run time was spent in domain decomposition, 81: 0 % 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: 12 % 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: 1.196 0.622 192.3 81: (ns/day) (hour/ns) 81: Performance: 1.250 19.197 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 (1547 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: 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: 22 % of the run time was spent in domain decomposition, 81: 0 % 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: 11 % 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: 0.889 0.445 200.0 81: (ns/day) (hour/ns) 81: Performance: 1.749 13.723 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 (1287 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: 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: 1.2%. 81: The balanceable part of the MD step is 42%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.5%. 81: 81: 81: NOTE: 26 % 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: 0.002 0.001 189.5 81: (ns/day) (hour/ns) 81: Performance: 941.675 0.025 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 (52 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: 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: 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: 0.001 0.001 188.8 81: (ns/day) (hour/ns) 81: Performance: 1013.515 0.024 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 (67 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: 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: 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: 0.001 0.001 187.9 81: (ns/day) (hour/ns) 81: Performance: 1013.043 0.024 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 (199 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: 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: 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: 0.002 0.001 188.6 81: (ns/day) (hour/ns) 81: Performance: 948.797 0.025 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 (39 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: 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: 10 % of the run time was spent in domain decomposition, 81: 0 % 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: 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: 1.412 0.722 195.6 81: (ns/day) (hour/ns) 81: Performance: 1.077 22.283 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 (1717 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: 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: 0.001 0.001 189.0 81: (ns/day) (hour/ns) 81: Performance: 1049.048 0.023 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 (51 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: 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: 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: 0.001 0.001 188.5 81: (ns/day) (hour/ns) 81: Performance: 1034.737 0.023 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 (232 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: 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: 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: 0.001 0.001 188.6 81: (ns/day) (hour/ns) 81: Performance: 1007.877 0.024 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 (63 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: 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: 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: 0.001 0.001 188.7 81: (ns/day) (hour/ns) 81: Performance: 1035.065 0.023 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 (63 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: 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: 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: 0.001 0.001 188.1 81: (ns/day) (hour/ns) 81: Performance: 1030.975 0.023 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 (71 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: 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: 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: 0.001 0.001 188.8 81: (ns/day) (hour/ns) 81: Performance: 1020.971 0.024 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 (55 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 (9002 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 37 tests from 2 test suites ran. (9018 ms total) 81: [ PASSED ] 37 tests. 81/81 Test #81: MdrunVirtualSiteTests .......................... Passed 9.06 sec 100% tests passed, 0 tests failed out of 81 Label Time Summary: GTest = 280.39 sec*proc (79 tests) IntegrationTest = 250.56 sec*proc (23 tests) MpiTest = 187.27 sec*proc (19 tests) QuickGpuTest = 15.36 sec*proc (15 tests) SlowTest = 27.67 sec*proc (13 tests) UnitTest = 2.15 sec*proc (43 tests) Total Test time (real) = 280.49 sec /usr/bin/make -j12 -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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directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 62%] Built target argon-forces-integration [ 62%] Built target methane-water-integration cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/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-dp/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-dp' [ 62%] 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-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/external/googletest/googlemock /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/external/googletest/googlemock /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering 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/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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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build 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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.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/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 -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/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]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /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 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 -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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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/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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/awh_setup.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/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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/densityfitting.cpp.o -MF 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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 -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/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 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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-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-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-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 -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/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/calcvir.cpp 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-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/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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp 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/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-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/qmmm/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/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-dp' /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-dp' 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 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-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 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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../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 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/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 -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/basic-dp' [ 64%] Built target testutils-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 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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 -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/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/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 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-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 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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-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 -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 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 -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 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 -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-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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops 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-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/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 -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 -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/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 -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/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 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 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 -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' [ 64%] Built target nblib_test_infrastructure /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-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 -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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-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 -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/basic-dp/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_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 applied_forces-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/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 -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 -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-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 -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-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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/tests/testasserts_tests.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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 density_fitting_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 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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 -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/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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 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 -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-dp' [ 64%] Built target nonbonded-fep-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/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 -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF 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 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o 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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target mdrun_test_infrastructure 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 -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/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 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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 -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 /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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-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/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-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\" -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 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"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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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-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 -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 make[4]: Leaving 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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 [ 64%] Built target qmmm_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-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 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'/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target nbnxm-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target testutils-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 -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 -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-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 /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /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-dp' 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 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-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 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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 -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.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-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 -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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/basic-dp' [ 65%] 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-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/math/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= 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 -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 -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/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 -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/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/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 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 -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/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 -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/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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 65%] 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 src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-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/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 /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 -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-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\" 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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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/expanded.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 -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/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 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-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 -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 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 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-std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-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/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 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/usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 /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 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops 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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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-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/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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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/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 -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 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/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 -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 [ 68%] Built target onlinehelp-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 -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-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 -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/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 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-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 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-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 -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-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 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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\" 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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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../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 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/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 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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/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 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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 -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-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 -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 CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/gammadistribution.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 69%] Built target restraintpotential-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 -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/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 -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-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 -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 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 -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-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 -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 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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/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/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 -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 /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 70%] Built target gpu_utils-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-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= 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 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-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 -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/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 -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/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 -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/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 -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/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 -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-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 -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-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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 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/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 -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 [ 70%] Built target timing-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 -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 -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/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 -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-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 -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 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 -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/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 -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_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/settletestrunners_gpu.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 -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/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_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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-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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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/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 -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-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 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-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 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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/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 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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 -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 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 -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/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 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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 -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-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 -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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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-dp' [ 73%] Built target mdlib-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 /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests/entropy.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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 73%] 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/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 -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 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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-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../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 -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 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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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' 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 -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 [ 74%] Built target ewald-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 -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/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 -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/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 -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/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 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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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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/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= 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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/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_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 mdtypes-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 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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/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 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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/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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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 pdb2gmx1-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/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 -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 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/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 -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/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 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/keyvaluetreetransform.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 -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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 77%] Built target pdb2gmx3-test 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/neldermead.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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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/basic-dp' [ 77%] 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 -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/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 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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/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 78%] Built target random-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 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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-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 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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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 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/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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops 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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 -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 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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 -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/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 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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 -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/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 -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-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 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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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 80%] Built target energyanalysis-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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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/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 -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 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-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 src/programs/mdrun/tests/CMakeFiles/mdrun-output-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 -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-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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/topdirs.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 -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/gromacs/options/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/timeunitmanager.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 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-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 -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/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 -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/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 -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 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 -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/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 -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/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 -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/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_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 81%] Built target gmxpreprocess-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 /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -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/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 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 81%] Built target analysisdata-test-shared /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 -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 -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-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 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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 -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/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 -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/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 -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/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 -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 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 -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-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 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-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-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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o 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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/cmake -E cmake_link_script CMakeFiles/tool-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/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_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-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 -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 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-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 -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/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 -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/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 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-c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/poscalc.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 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CMakeFiles/mdrun-modules-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/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 -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/basic-dp/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_d.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-modules-test /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= 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 -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/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /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' /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 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 /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 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 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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 -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 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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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-output-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-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-tpi-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-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 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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 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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-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 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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 -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 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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 -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 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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/xvgio.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target mdrun-tpi-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 -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-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 -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 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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 84%] Built target fileio-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 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 -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 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= 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 -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 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 -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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 84%] Built target coordinateio-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 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 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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/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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../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../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 -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/__/__/__/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/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 -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-dp' [ 85%] Built target selection-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= 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 -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 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 /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 -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-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_d.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-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_d.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 85%] Built target mdrun-mpi-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= 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 -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 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 /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-coupling-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-dp' [ 85%] Built target mdrun-multisim-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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 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 -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-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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-dp' [ 86%] Built target mdrun-io-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 src/programs/mdrun/tests/CMakeFiles/mdrun-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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 86%] Built target mdrun-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 -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/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 -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 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 -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/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 -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/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-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-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/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_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../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 -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' [ 88%] 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/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 -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-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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 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 [ 89%] Built target mdrun-mpi-pme-test make[4]: Entering 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/depend 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]: 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 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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/virtualsites.cpp 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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/integrator.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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../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 -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/basic-dp' [ 90%] Built target simd-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 -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 -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 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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 90%] Built target mdrun-fep-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 -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/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 -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-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 -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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\" -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 -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 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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 [ 90%] Built target mdrun-non-integrator-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 -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-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 -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-dp' [ 90%] Built target mdrun-multisim-replex-equivalence-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-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 -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\" -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 -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/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 -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-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 -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/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-constraints-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 mdrun-mpi-coordination-basic-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 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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/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 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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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 92%] 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 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 -Wno-missing-field-initializers -fexcess-precision=fast 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'/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 92%] Built target mdrun-mpi-coordination-constraints-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 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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 -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 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 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-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/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 -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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 92%] Built target mdrun-simulator-comparison-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 -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/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 -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-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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 -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-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 [ 92%] Built target nblib-integrator-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 92%] Built target nblib-tpr-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 -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' [ 93%] Built target mdrun-vsites-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 -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/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 -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/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 -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/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 -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/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 -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/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 -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-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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/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 -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 CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/typetraits.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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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' 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 -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 [ 94%] Built target mdrun-pull-test 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 -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-dp' [ 94%] Built target mdrunutility-test 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 -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 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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-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/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 -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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 94%] Built target mdrunutility-mpi-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 -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 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 -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 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 -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-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 -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/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 94%] Built target nblib-util-test 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 -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-dp/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" "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_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/lifetime.cpp 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:118:9: warning: iteration 2147483647 invokes undefined behavior [-Waggressive-loop-optimizations] 118 | for (int i = 0; i < count; ++i) | ^~~ /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/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 -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/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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/pargs.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 97%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/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_d.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 97%] Built target analysisdata-test 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 97%] Built target commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 98%] Built target nblib-listed-forces-test 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [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/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' [100%] Built target nblib-tests /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 (0 ms) 1: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 1: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 1: [ RUN ] NBlibTest.EndToEndListedComparison 1: [ OK ] NBlibTest.EndToEndListedComparison (1 ms) 1: [ RUN ] NBlibTest.shiftForcesAreCorrect 1: [ OK ] NBlibTest.shiftForcesAreCorrect (32 ms) 1: [----------] 8 tests from NBlibTest (34 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 (0 ms) 1: [----------] 1 test from LinearChainDataFixture (0 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. (38 ms total) 1: [ PASSED ] 44 tests. 1/81 Test #1: NbLibListedForcesTests ......................... Passed 0.07 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 0.02 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 0.02 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 0.02 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 (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. (3 ms total) 5: [ PASSED ] 56 tests. 5/81 Test #5: NbLibSetupTests ................................ Passed 0.04 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 (12 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 (8 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 (7 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 (7 ms) 6: [----------] 4 tests from TprReaderTest (36 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 4 tests from 1 test suite ran. (51 ms total) 6: [ PASSED ] 4 tests. 6/81 Test #6: NbLibTprTests .................................. Passed 0.07 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 (1 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 (8 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 20 tests from 1 test suite ran. (8 ms total) 7: [ PASSED ] 20 tests. 7/81 Test #7: NbLibIntegrationTests .......................... Passed 0.03 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 0.02 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 (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 (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 (6 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 (1 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 59 tests from 5 test suites ran. (12 ms total) 9: [ PASSED ] 59 tests. 9/81 Test #9: TestUtilsUnitTests ............................. Passed 0.03 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 (0 ms) 10: [----------] 1 test from MpiSelfTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/81 Test #10: TestUtilsMpiUnitTests .......................... Passed 0.02 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 (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 (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 (0 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 (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 (0 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 (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. (10 ms total) 11: [ PASSED ] 386 tests. 11: 11: YOU HAVE 1 DISABLED TEST 11: 11/81 Test #11: UtilityUnitTests ............................... Passed 0.05 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 (0 ms) 12: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 12: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 12: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 2 tests from 1 test suite ran. (1 ms total) 12: [ PASSED ] 2 tests. 12/81 Test #12: UtilityMpiUnitTests ............................ Passed 0.02 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 (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 (13 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 72 tests from 1 test suite ran. (13 ms total) 13: [ PASSED ] 72 tests. 13/81 Test #13: GmxlibTests .................................... Passed 0.05 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 (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 (2 ms) 14: [ RUN ] PrEbinTest.HandlesEmptyAverages 14: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 14: [----------] 2 tests from PrEbinTest (3 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 (6 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (5 ms) 14: [----------] 14 tests from WithParameters/ConstraintsTest (16 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 (1 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 (0 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 (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-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 (5 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 14: [----------] 11 tests from WithParameters/EnergyOutputTest (19 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 (3 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 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 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 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) 14: [----------] 16 tests from WithParameters/LeapFrogTest (14 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 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 14: [----------] 13 tests from WithParameters/SettleTest (5 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 155 tests from 17 test suites ran. (63 ms total) 14: [ PASSED ] 155 tests. 14/81 Test #14: MdlibUnitTest .................................. Passed 0.10 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 (2 ms) 15: [----------] 1 test from biasGridTest (2 ms total) 15: 15: [----------] 1 test from BiasSharingTest 15: [ RUN ] BiasSharingTest.SharingWorks 15: [ OK ] BiasSharingTest.SharingWorks (1 ms) 15: [----------] 1 test from BiasSharingTest (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 (3 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 (6 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 (8 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (8 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (7 ms) 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (34 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 21 tests from 8 test suites ran. (50 ms total) 15: [ PASSED ] 21 tests. 15/81 Test #15: AwhTest ........................................ Passed 0.07 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 (1 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 18 tests from 4 test suites ran. (2 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 234356717 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 (6 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 -84705285 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-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 -16791673 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 (5 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 -8430849 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 (18 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 -302383209 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 (15 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 2130696163 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 (4 ms) 17: [----------] 7 tests from QMMMTopologyPreprocessorTest (57 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. (60 ms total) 17: [ PASSED ] 21 tests. 17/81 Test #17: QMMMAppliedForcesUnitTest ...................... Passed 0.08 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 0.02 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 (5 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 (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 (0 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 0.06 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 0.02 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 (1 ms) 21: [----------] 3 tests from CommandLineHelpModuleTest (2 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 (1 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. (8 ms total) 21: [ PASSED ] 60 tests. 21/81 Test #21: CommandLineUnitTests ........................... Passed 0.03 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 0.02 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 (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 (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 4 tests from 1 test suite ran. (2 ms total) 23: [ PASSED ] 4 tests. 23/81 Test #23: DomDecMpiTests ................................. Passed 0.04 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 (4 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 (1 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 (1 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 (1 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 (1 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 (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 (1 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 (2 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 (1 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 (2 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 (2 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 (0 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 (1 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 (2 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 (2 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (1 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 (1 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 (0 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 (1 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 (1 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 (0 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 (1 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 (1 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 (1 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 (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 (0 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 (0 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 (0 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 (1 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 (1 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 (1 ms) 24: [----------] 108 tests from Pme_SplineAndSpreadTest (103 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_ (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_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_ (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_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 (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 (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 (8 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 (2 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 (4 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_ (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_ (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 (7 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 (8 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 (1 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 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 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (0 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 (0 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 (0 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 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (0 ms) 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (21 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 407 tests from 9 test suites ran. (158 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 0.20 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 (4 ms) 25: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (7 ms) 25: [----------] 2 tests from ManyFFTTest (12 ms total) 25: 25: [----------] 1 test from FFTTest 25: [ RUN ] FFTTest.Real2DLength18_15Test 25: [ OK ] FFTTest.Real2DLength18_15Test (2 ms) 25: [----------] 1 test from FFTTest (2 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 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 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 (3 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (4 ms) 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (14 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 (0 ms) 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) 25: [----------] 2 tests from Works/ParameterizedFFTTest3D (2 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 15 tests from 4 test suites ran. (31 ms total) 25: [ PASSED ] 15 tests. 25/81 Test #25: FFTUnitTests ................................... Passed 0.06 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. (1 ms total) 26: [ PASSED ] 64 tests. 26/81 Test #26: GpuUtilsUnitTests .............................. Passed 0.04 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 (0 ms) 27: [----------] 1 test from CpuInfoTest (0 ms total) 27: 27: [----------] 4 tests from HardwareTopologyTest 27: [ RUN ] HardwareTopologyTest.Execute 27: [ OK ] HardwareTopologyTest.Execute (14 ms) 27: [ RUN ] HardwareTopologyTest.HwlocExecute 27: [ OK ] HardwareTopologyTest.HwlocExecute (14 ms) 27: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 27: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (12 ms) 27: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 27: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (10 ms) 27: [----------] 4 tests from HardwareTopologyTest (52 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 (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 (4 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 (3 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 (1 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 (0 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 (1 ms) 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 27: 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 27: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 21 tests from 9 test suites ran. (67 ms total) 27: [ PASSED ] 21 tests. 27/81 Test #27: HardwareUnitTests .............................. Passed 0.09 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 (30 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (22 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 28: [----------] 12 tests from DensitySimilarityTest (55 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 (1 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. (59 ms total) 28: [ PASSED ] 301 tests. 28/81 Test #28: MathUnitTests .................................. Passed 0.09 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 (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 29: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 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 (4 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 17 tests from 1 test suite ran. (4 ms total) 29: [ PASSED ] 17 tests. 29/81 Test #29: MdrunUtilityUnitTests .......................... Passed 0.02 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 (2 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 30: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (2 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 30: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (1 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 (1 ms) 30: [----------] 6 tests from ThreadAffinityMultiRankTest (8 ms total) 30: 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (1 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (13 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (1 ms) 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (21 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 13 tests from 2 test suites ran. (30 ms total) 30: [ PASSED ] 13 tests. 30/81 Test #30: MdrunUtilityMpiUnitTests ....................... Passed 0.05 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 0.02 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 (7 ms) 32: [----------] 2 tests from CheckpointDataTest (8 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 (2 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 (5 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. (15 ms total) 32: [ PASSED ] 93 tests. 32/81 Test #32: MdtypesUnitTest ................................ Passed 0.04 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 0.02 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 (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 111 tests from 18 test suites ran. (6 ms total) 34: [ PASSED ] 111 tests. 34/81 Test #34: OptionsUnitTests ............................... Passed 0.03 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 (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 (7 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 0.03 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 0.03 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 (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 (25 ms) 38: [ RUN ] SplineTableTest/0.ThreeFunctions 38: [ OK ] SplineTableTest/0.ThreeFunctions (20 ms) 38: [ RUN ] SplineTableTest/0.Simd 38: [ OK ] SplineTableTest/0.Simd (3 ms) 38: [ RUN ] SplineTableTest/0.SimdTwoFunctions 38: [ OK ] SplineTableTest/0.SimdTwoFunctions (14 ms) 38: [----------] 10 tests from SplineTableTest/0 (84 ms total) 38: 38: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 38: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 38: [ RUN ] SplineTableTest/1.Sinc 38: [ OK ] SplineTableTest/1.Sinc (0 ms) 38: [ RUN ] SplineTableTest/1.LJ12 38: [ OK ] SplineTableTest/1.LJ12 (16 ms) 38: [ RUN ] SplineTableTest/1.PmeCorrection 38: [ OK ] SplineTableTest/1.PmeCorrection (0 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 (28 ms) 38: [ RUN ] SplineTableTest/1.ThreeFunctions 38: [ OK ] SplineTableTest/1.ThreeFunctions (28 ms) 38: [ RUN ] SplineTableTest/1.Simd 38: [ OK ] SplineTableTest/1.Simd (5 ms) 38: [ RUN ] SplineTableTest/1.SimdTwoFunctions 38: [ OK ] SplineTableTest/1.SimdTwoFunctions (23 ms) 38: [----------] 10 tests from SplineTableTest/1 (104 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 20 tests from 2 test suites ran. (188 ms total) 38: [ PASSED ] 20 tests. 38/81 Test #38: TableUnitTests ................................. Passed 0.21 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 (2 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. (3 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-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 0.02 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 (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 0.02 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. (0 ms total) 42: [ PASSED ] 8 tests. 42/81 Test #42: PullTest ....................................... Passed 0.02 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 (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 (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 (3 ms) 43: [ RUN ] SimdMathTest.log2 43: [ OK ] SimdMathTest.log2 (1 ms) 43: [ RUN ] SimdMathTest.log 43: [ OK ] SimdMathTest.log (1 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 (0 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 (0 ms) 43: [ RUN ] SimdMathTest.atan2 43: [ OK ] SimdMathTest.atan2 (0 ms) 43: [ RUN ] SimdMathTest.pmeForceCorrection 43: [ OK ] SimdMathTest.pmeForceCorrection (0 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 (1 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 (1 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 43: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracy 43: [ OK ] SimdMathTest.expSingleAccuracy (1 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 (0 ms) 43: [ RUN ] SimdMathTest.erfcSingleAccuracy 43: [ OK ] SimdMathTest.erfcSingleAccuracy (0 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 (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 (1 ms) 43: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 43: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 43: [----------] 56 tests from SimdMathTest (57 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. (59 ms total) 43: [ PASSED ] 247 tests. 43/81 Test #43: SimdUnitTests .................................. Passed 0.08 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 0.01 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 (422 ms) 45: [----------] 1 test from GmxChiTest (466 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 (9 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 (4 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 (17 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 (0 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 (0 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 (0 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 (0 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 (0 ms) 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (3 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 22 tests from 4 test suites ran. (488 ms total) 45: [ PASSED ] 22 tests. 45/81 Test #45: GmxAnaTest ..................................... Passed 0.51 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 (1 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/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 -381747787 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 (282 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 -729842377 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 (229 ms) 46: [----------] 2 tests from GenionTest (512 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 (0 ms) 46: [----------] 1 test from GenRestrTest (0 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 -1157663753 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 -687866546 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 (2 ms) 46: [----------] 1 test from GromppDirectiveTest (2 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 (0 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 (0 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 (3 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 (0 ms) 46: [----------] 5 tests from InsertMoleculesTest (6 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 (1 ms) 46: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 46: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (8 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 (1 ms) 46: [ RUN ] GetIrTest.RejectsValueWithoutKey 46: [ OK ] GetIrTest.RejectsValueWithoutKey (9 ms) 46: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 46: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (9 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 46: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 46: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (5 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 (1 ms) 46: [ RUN ] GetIrTest.RejectsImplicitSolventYes 46: [ OK ] GetIrTest.RejectsImplicitSolventYes (8 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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/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 (1 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 (1 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 (1 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 (1 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 (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 46: [----------] 34 tests from GetIrTest (79 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 (4 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 (22 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 (21 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 (10 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 (91 ms) 46: [----------] 5 tests from SolvateTest (150 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. (756 ms total) 46: [ PASSED ] 72 tests. 46/81 Test #46: GmxPreprocessTests ............................. Passed 0.78 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 (55 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 (36 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 (26 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 (22 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 (100 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 (24 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 (26 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 (24 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 (22 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 (111 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 (22 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 (24 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 (22 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 (20 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 (98 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 (24 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 (26 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 (24 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 (22 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 (111 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 (22 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 (24 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 (22 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 (20 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 (99 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 (24 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 (26 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 (24 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 (22 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 (111 ms) 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1248 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 30 tests from 1 test suite ran. (1248 ms total) 47: [ PASSED ] 30 tests. 47/81 Test #47: Pdb2gmx1Test ................................... Passed 1.27 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 (51 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 (33 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 (23 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 (20 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 (53 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 (20 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 (23 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 (20 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 (20 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 (54 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 (20 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 (22 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 (20 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 (19 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 (51 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 (20 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 (22 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 (20 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 (19 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 (54 ms) 48: [----------] 20 tests from G43a1/Pdb2gmxTest (593 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 (21 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 (24 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 (22 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 (21 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 (54 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 (22 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 (25 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 (22 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 (22 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 (56 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 (22 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 (24 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 (22 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 (21 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 (54 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 (22 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 (25 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 (23 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 (22 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 (56 ms) 48: [----------] 20 tests from G53a6/Pdb2gmxTest (588 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 40 tests from 2 test suites ran. (1182 ms total) 48: [ PASSED ] 40 tests. 48/81 Test #48: Pdb2gmx2Test ................................... Passed 1.20 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 (60 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 (37 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 (27 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 (22 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 (90 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 (25 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 (27 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 (25 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 (23 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 (99 ms) 49: [----------] 10 tests from Amber/Pdb2gmxTest (441 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 (9 ms) 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest (9 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 (22 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 (24 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 (22 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 (21 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 (85 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 (10 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 (24 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 (26 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 (24 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 (22 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 (95 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 (10 ms) 49: [----------] 12 tests from Charmm/Pdb2gmxTest (393 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 (23 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 (18 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 (23 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 (18 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 (22 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 (19 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 (22 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 (18 ms) 49: [----------] 8 tests from ChainSep/Pdb2gmxTest (167 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 (12 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 (12 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 (12 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 (12 ms) 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest (51 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 (673 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 (77 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 (1334 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 (76 ms) 49: [----------] 4 tests from Cyclic/Pdb2gmxTest (2162 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 39 tests from 6 test suites ran. (3226 ms total) 49: [ PASSED ] 39 tests. 49/81 Test #49: Pdb2gmx3Test ................................... Passed 3.25 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 (11 ms) 50: [ RUN ] AutocorrTest.EacNoNormalize 50: [ OK ] AutocorrTest.EacNoNormalize (5 ms) 50: [ RUN ] AutocorrTest.EacCos 50: [ OK ] AutocorrTest.EacCos (14 ms) 50: [ RUN ] AutocorrTest.EacVector 50: [ OK ] AutocorrTest.EacVector (16 ms) 50: [ RUN ] AutocorrTest.EacRcross 50: [ OK ] AutocorrTest.EacRcross (1 ms) 50: [ RUN ] AutocorrTest.EacP0 50: [ OK ] AutocorrTest.EacP0 (14 ms) 50: [ RUN ] AutocorrTest.EacP1 50: [ OK ] AutocorrTest.EacP1 (15 ms) 50: [ RUN ] AutocorrTest.EacP2 50: [ OK ] AutocorrTest.EacP2 (33 ms) 50: [ RUN ] AutocorrTest.EacP3 50: [ OK ] AutocorrTest.EacP3 (4 ms) 50: [ RUN ] AutocorrTest.EacP4 50: [ OK ] AutocorrTest.EacP4 (15 ms) 50: [----------] 10 tests from AutocorrTest (134 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 (5 ms) 50: [ RUN ] ExpfitTest.EffnEXP7 50: [ OK ] ExpfitTest.EffnEXP7 (4 ms) 50: [ RUN ] ExpfitTest.EffnEXP9 50: [ OK ] ExpfitTest.EffnEXP9 (18 ms) 50: [ RUN ] ExpfitTest.EffnERF 50: [ OK ] ExpfitTest.EffnERF (1 ms) 50: [ RUN ] ExpfitTest.EffnERREST 50: [ OK ] ExpfitTest.EffnERREST (2 ms) 50: [ RUN ] ExpfitTest.EffnVAC 50: [ OK ] ExpfitTest.EffnVAC (14 ms) 50: [ RUN ] ExpfitTest.EffnPRES 50: [ OK ] ExpfitTest.EffnPRES (10 ms) 50: [----------] 10 tests from ExpfitTest (59 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. (199 ms total) 50: [ PASSED ] 21 tests. 50/81 Test #50: CorrelationsTest ............................... Passed 0.21 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 (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 (2 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 (2 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 (0 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 (3 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 (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 (3 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 (0 ms total) 51: 51: [----------] 6 tests from AverageModuleTest 51: [ RUN ] AverageModuleTest.BasicTest 51: [ OK ] AverageModuleTest.BasicTest (0 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 (4 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 (0 ms) 51: [----------] 2 tests from FrameAverageModuleTest (1 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 (0 ms) 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [----------] 2 tests from SimpleHistogramModuleTest (1 ms total) 51: 51: [----------] 3 tests from WeightedHistogramModuleTest 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 51: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 51: [----------] 3 tests from WeightedHistogramModuleTest (2 ms total) 51: 51: [----------] 3 tests from BinAverageModuleTest 51: [ RUN ] BinAverageModuleTest.ComputesCorrectly 51: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 51: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 51: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 51: [----------] 3 tests from BinAverageModuleTest (1 ms total) 51: 51: [----------] 4 tests from AbstractAverageHistogramTest 51: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 51: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 51: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 51: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 51: [----------] 4 tests from AbstractAverageHistogramTest (3 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 (0 ms) 51: [----------] 3 tests from LifetimeModuleTest (1 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 69 tests from 14 test suites ran. (31 ms total) 51: [ PASSED ] 69 tests. 51/81 Test #51: AnalysisDataUnitTests .......................... Passed 0.05 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 (7 ms) 52: [----------] 1 test from OutputSelectorDeathTest (7 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 (4 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 (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 (9 ms) 52: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 52: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 52: [----------] 5 tests from TrajectoryFrameWriterTest (23 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 (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 (4 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 (3 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 (3 ms) 52: [----------] 5 tests from SetAtomsTest (21 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 (3 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 (3 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 (2 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 (2 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 (2 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 (2 ms) 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (18 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 (2 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 (2 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 (2 ms) 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (8 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 (5 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 (5 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 (4 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 (4 ms) 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (19 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 (1 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 (1 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 (1 ms) 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (5 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 (2 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 (1 ms) 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (3 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 (1 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 (1 ms) 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (3 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 (2 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 (1 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 (1 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 (1 ms) 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput (7 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 64 tests from 19 test suites ran. (120 ms total) 52: [ PASSED ] 64 tests. 52/81 Test #52: CoordinateIOTests .............................. Passed 0.14 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 (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 (3 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 (3 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 (3 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 (3 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 (3 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 (2 ms) 53: [----------] 11 tests from AngleModuleTest (40 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 (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 (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 (1 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 (9 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 (2 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 (2 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (6 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 (9 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 (8 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 (1 ms) 53: [----------] 4 tests from ConvertTrjModuleTest (21 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 (2 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 (2 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 (2 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 (5 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 (5 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 (5 ms) 53: [----------] 6 tests from DistanceModuleTest (25 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 (1 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 (1 ms) 53: [----------] 2 tests from ExtractClusterModuleTest (2 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 (45 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 (43 ms) 53: [----------] 2 tests from FreeVolumeModuleTest (88 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 (1 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 (1 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 (1 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 (1 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 1853881854 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 (13 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 1572609503 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 (13 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 -156287112 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 (12 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 -211920897 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 (12 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 -814229069 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 (12 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 2142756860 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 (12 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 -675989507 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 (12 ms) 53: [----------] 11 tests from MsdModuleTest (96 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 9 tests from PairDistanceModuleTest (12 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 (12 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 (8 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 (12 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 (7 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 (14 ms) 53: [----------] 5 tests from RdfModuleTest (56 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 (6 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 (3 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 (3 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 (4 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 (4 ms) 53: [----------] 5 tests from SasaModuleTest (22 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 (2 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 8 tests from SelectModuleTest (13 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 (0 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 53: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 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 (0 ms) 53: [ RUN ] SurfaceAreaTest.Computes100Points 53: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 53: [----------] 10 tests from SurfaceAreaTest (4 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 (1 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 (1 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 1073149947 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 (258 ms) 53: [----------] 4 tests from TopologyInformation (261 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 4 tests from TrajectoryModuleTest (6 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. (669 ms total) 53: [ PASSED ] 96 tests. 53/81 Test #53: TrajectoryAnalysisUnitTests .................... Passed 0.69 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 (11 ms) 54: [----------] 1 test from DhdlTest (12 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 (14 ms) 54: [----------] 1 test from OriresTest (15 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 (3 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 (3 ms) 54: [----------] 3 tests from EnergyTest (10 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 (15 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 (16 ms) 54: [----------] 2 tests from ViscosityTest (32 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 7 tests from 4 test suites ran. (70 ms total) 54: [ PASSED ] 7 tests. 54/81 Test #54: EnergyAnalysisUnitTests ........................ Passed 0.09 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 -557877505 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 = -557877505 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[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 55: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 55: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 55: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 55: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 55: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 55: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 55: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 55: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 55: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 55: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 55: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 55: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 55: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 55: functype[79]=LJ_SR, c6= 1.24956934e-03, 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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, 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= 4.39320000e+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 (5 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 (0 ms) 55: [----------] 2 tests from DumpTest (6 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 (0 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 -1141916945 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 (0 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 (0 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 -137409122 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 (242 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 -1078024371 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 (234 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 1266612979 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 (234 ms) 55: [----------] 3 tests from ConvertTprTest (711 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 (0 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 (0 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 (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 (0 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 (4 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 (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 (0 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 (0 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 (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 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 (0 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 (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 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 (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 (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 (7 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 54 tests from 6 test suites ran. (1263 ms total) 55: [ PASSED ] 54 tests. 55/81 Test #55: ToolUnitTests .................................. Passed 1.29 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 (0 ms) 56: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 56: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 56: [----------] 2 tests from FileMD5Test (0 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 (0 ms) 56: [----------] 4 tests from MrcDensityMap (0 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 (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 42 tests from 10 test suites ran. (2 ms total) 56: [ PASSED ] 42 tests. 56/81 Test #56: FileIOTests .................................... Passed 0.01 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 (2 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 (21 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 57: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (17 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchBox 57: [ OK ] NeighborhoodSearchTest.GridSearchBox (2 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 57: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (7 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 57: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (3 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 57: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 57: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (2 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (26 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 (2 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 57: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 57: [----------] 15 tests from NeighborhoodSearchTest (84 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 (1 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 (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 (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 (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 (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 (8 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 (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 (4 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 (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 (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 (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 (0 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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 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 (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 57: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 57: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 57: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 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 (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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 57: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 57: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 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 (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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 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 (0 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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 57: [----------] 70 tests from SelectionCollectionDataTest (32 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 (3 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 (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 (1 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 201 tests from 11 test suites ran. (141 ms total) 57: [ PASSED ] 201 tests. 57/81 Test #57: SelectionUnitTests ............................. Passed 0.16 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 (17 ms) 58: [----------] 1 test from MdrunTest (17 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: 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 2147215091 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 0.002 195.3 58: (ns/day) (hour/ns) 58: Performance: 70.027 0.343 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 (10 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: 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 -571605281 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: 0.001 0.001 184.8 58: (ns/day) (hour/ns) 58: Performance: 273.088 0.088 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 (7 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: 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 -9576452 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: 0.001 0.001 185.2 58: (ns/day) (hour/ns) 58: Performance: 283.226 0.085 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 (6 ms) 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (24 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: 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: 0.002 0.001 191.1 58: (ns/day) (hour/ns) 58: Performance: 1669.085 0.014 58: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (5 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: 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: 0.003 0.001 196.2 58: (ns/day) (hour/ns) 58: Performance: 1020.135 0.024 58: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (6 ms) 58: [----------] 2 tests from Argon12/OutputFiles (11 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: 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 -390594563 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: 0.006 0.003 197.1 58: (ns/day) (hour/ns) 58: Performance: 195.734 0.123 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (7 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: 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 2122049175 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 0.002 174.9 58: (ns/day) (hour/ns) 58: Performance: 267.304 0.090 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (6 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: 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 -620767265 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 0.001 194.6 58: (ns/day) (hour/ns) 58: Performance: 405.226 0.059 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (5 ms) 58: [----------] 3 tests from MdrunCanWrite/Trajectories (20 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: 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 -1955889297 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: 0.001 0.001 190.0 58: (ns/day) (hour/ns) 58: Performance: 381.060 0.063 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (4 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: 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 -281084953 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: 0.001 0.001 189.6 58: (ns/day) (hour/ns) 58: Performance: 386.204 0.062 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (4 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: 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 -286327041 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: 0.001 0.001 189.5 58: (ns/day) (hour/ns) 58: Performance: 394.328 0.061 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (4 ms) 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories (13 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 12 tests from 5 test suites ran. (129 ms total) 58: [ PASSED ] 12 tests. 58/81 Test #58: MdrunOutputTests ............................... Passed 0.15 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: 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 = -3.85652608067156e+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 -1109394089 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 (4 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 59: Number of degrees of freedom in T-Coupling group rest is 33.00 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 -556732737 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 (3 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 (7 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 59: Number of degrees of freedom in T-Coupling group rest is 33.00 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 = 7.47247842297763e+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 -1025321 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 (5 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: 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 = -3.85652608067156e+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 -591617042 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 (5 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 59: Number of degrees of freedom in T-Coupling group rest is 33.00 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 = 6.78276506555709e+03 on atom 2 59: Norm of force = 1.96088641457984e+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 -545342865 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 (5 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 -8388806 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (8 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: 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 -348667969 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: 0.003 0.002 194.7 59: (ns/day) (hour/ns) 59: Performance: 148.804 0.161 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: 0.001 0.001 187.4 59: (ns/day) (hour/ns) 59: Performance: 651.308 0.037 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 (9 ms) 59: [----------] 9 tests from DensityFittingTest (57 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: 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: 0.000 0.000 187.6 59: (ns/day) (hour/ns) 59: Performance: 369.030 0.065 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 -4287233 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 (5 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: 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: 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: 0.000 0.000 185.7 59: (ns/day) (hour/ns) 59: Performance: 431.414 0.056 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 -268503298 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 (4 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: 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: 17 % 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: 0.000 0.000 186.3 59: (ns/day) (hour/ns) 59: Performance: 428.861 0.056 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 2141010911 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 (4 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: 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: 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 0.000 192.7 59: (ns/day) (hour/ns) 59: Performance: 240.949 0.100 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 -450895885 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 (12 ms) 59: [----------] 4 tests from MimicTest (26 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: 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 36137. 59: IMD: -imdwait not set, starting simulation. 59: starting mdrun 'Glycine' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to -164374 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: 0.001 0.001 187.2 59: (ns/day) (hour/ns) 59: Performance: 957.010 0.025 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (65 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: 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 58019. 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 1696571038 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 (63 ms) 59: [----------] 2 tests from WithIntegrator/ImdTest (129 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 15 tests from 3 test suites ran. (239 ms total) 59: [ PASSED ] 15 tests. 59/81 Test #59: MdrunModulesTests .............................. Passed 0.25 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 -1099727505 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-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 -323005505 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-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 1862269902 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 (4 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 -5013633 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 (7 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 -423715205 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 (7 ms) 60: [----------] 5 tests from GromppTest (31 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: 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 -1721877 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: 0.004 0.002 193.7 60: (ns/day) (hour/ns) 60: Performance: 121.011 0.198 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: 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: 0.001 0.001 185.3 60: (ns/day) (hour/ns) 60: Performance: 360.705 0.067 60: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (12 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: 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 7: Run time exceeded 0.000 hours, will terminate the run within 2 steps 60: Setting the LD random seed to -536871986 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: 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: 0.002 0.001 187.1 60: (ns/day) (hour/ns) 60: Performance: 870.427 0.028 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: 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 8, 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: 0.005 0.003 194.2 60: (ns/day) (hour/ns) 60: Performance: 3130.283 0.008 60: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (12 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: 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 -135858647 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 0.001 188.7 60: (ns/day) (hour/ns) 60: Performance: 272.540 0.088 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: 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: 0.001 0.001 191.3 60: (ns/day) (hour/ns) 60: Performance: 432.100 0.056 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: 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: 0.001 0.001 191.0 60: (ns/day) (hour/ns) 60: Performance: 455.834 0.053 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: 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: 0.001 0.001 191.2 60: (ns/day) (hour/ns) 60: Performance: 462.820 0.052 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: 21 % 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 0.000 168.5 60: (ns/day) (hour/ns) 60: Performance: 614.217 0.039 60: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (19 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: 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 -72353829 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: 0.001 0.001 184.4 60: (ns/day) (hour/ns) 60: Performance: 487.080 0.049 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: 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: 0.001 0.001 185.8 60: (ns/day) (hour/ns) 60: Performance: 715.333 0.034 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (8 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: 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 -33752577 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: 0.001 0.000 184.9 60: (ns/day) (hour/ns) 60: Performance: 520.423 0.046 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 (5 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: 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 1744459771 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: 0.001 0.001 188.7 60: (ns/day) (hour/ns) 60: Performance: 366.789 0.065 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: 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: 0.001 0.000 191.5 60: (ns/day) (hour/ns) 60: Performance: 540.071 0.044 60: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (7 ms) 60: [----------] 6 tests from MdrunTerminationTest (66 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: 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: 0.001 0.001 190.8 60: (ns/day) (hour/ns) 60: Performance: 2013.924 0.012 60: trr version: GMX_trn_file (double precision) 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (5 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: 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: 0.002 0.001 195.1 60: (ns/day) (hour/ns) 60: Performance: 1280.256 0.019 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (5 ms) 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (10 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: 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: 0.002 0.001 193.2 60: (ns/day) (hour/ns) 60: Performance: 1615.258 0.015 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: 0.001 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 1310.362 0.018 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: 0.001 0.001 190.3 60: (ns/day) (hour/ns) 60: Performance: 1368.649 0.018 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: 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_secondpart.part0002.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 (10 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: 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: 0.002 0.001 195.4 60: (ns/day) (hour/ns) 60: Performance: 1591.062 0.015 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: 0.002 0.001 195.0 60: (ns/day) (hour/ns) 60: Performance: 821.741 0.029 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: 0.001 0.001 190.4 60: (ns/day) (hour/ns) 60: Performance: 1004.772 0.024 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 192.8 60: (ns/day) (hour/ns) 60: Performance: 2022.519 0.012 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: 0.001 0.001 191.2 60: (ns/day) (hour/ns) 60: Performance: 1411.290 0.017 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: 0.001 0.001 191.5 60: (ns/day) (hour/ns) 60: Performance: 1306.164 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 193.1 60: (ns/day) (hour/ns) 60: Performance: 2072.878 0.012 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: 0.001 0.001 191.6 60: (ns/day) (hour/ns) 60: Performance: 1365.212 0.018 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: 0.001 0.001 191.4 60: (ns/day) (hour/ns) 60: Performance: 1380.233 0.017 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.5 60: (ns/day) (hour/ns) 60: Performance: 2004.097 0.012 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: 0.001 0.001 189.6 60: (ns/day) (hour/ns) 60: Performance: 1421.748 0.017 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: 0.001 0.001 189.1 60: (ns/day) (hour/ns) 60: Performance: 1325.809 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.002 0.001 195.3 60: (ns/day) (hour/ns) 60: Performance: 1571.179 0.015 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: 0.001 0.001 194.2 60: (ns/day) (hour/ns) 60: Performance: 1013.830 0.024 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: 0.001 0.001 192.0 60: (ns/day) (hour/ns) 60: Performance: 1029.186 0.023 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 192.4 60: (ns/day) (hour/ns) 60: Performance: 2047.389 0.012 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: 0.001 0.001 190.3 60: (ns/day) (hour/ns) 60: Performance: 1406.421 0.017 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: 0.001 0.001 190.8 60: (ns/day) (hour/ns) 60: Performance: 1313.000 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.002 0.001 192.7 60: (ns/day) (hour/ns) 60: Performance: 1881.097 0.013 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: 0.001 0.001 191.2 60: (ns/day) (hour/ns) 60: Performance: 1324.194 0.018 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: 0.001 0.001 191.6 60: (ns/day) (hour/ns) 60: Performance: 1301.473 0.018 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: 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_secondpart.part0002.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 (10 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: 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: 0.004 0.002 195.3 60: (ns/day) (hour/ns) 60: Performance: 763.300 0.031 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: 0.003 0.002 194.5 60: (ns/day) (hour/ns) 60: Performance: 472.885 0.051 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: 0.002 0.001 193.1 60: (ns/day) (hour/ns) 60: Performance: 602.863 0.040 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: 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_secondpart.part0002.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 (27 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: 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: 0.004 0.002 195.7 60: (ns/day) (hour/ns) 60: Performance: 669.848 0.036 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: 0.003 0.001 193.7 60: (ns/day) (hour/ns) 60: Performance: 567.019 0.042 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: 0.003 0.001 193.4 60: (ns/day) (hour/ns) 60: Performance: 573.701 0.042 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: 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_secondpart.part0002.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 (25 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: 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: 0.004 0.002 195.9 60: (ns/day) (hour/ns) 60: Performance: 742.330 0.032 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: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 193.7 60: (ns/day) (hour/ns) 60: Performance: 596.469 0.040 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: 0.003 0.001 193.6 60: (ns/day) (hour/ns) 60: Performance: 596.578 0.040 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: 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_secondpart.part0002.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 (35 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: 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: 0.006 0.003 197.4 60: (ns/day) (hour/ns) 60: Performance: 460.846 0.052 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: 0.003 0.002 194.7 60: (ns/day) (hour/ns) 60: Performance: 491.114 0.049 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: 0.003 0.002 194.9 60: (ns/day) (hour/ns) 60: Performance: 494.090 0.049 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: 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_secondpart.part0002.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 (36 ms) 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (205 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: 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: 0.005 0.002 195.8 60: (ns/day) (hour/ns) 60: Performance: 609.899 0.039 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: 0.002 0.001 192.5 60: (ns/day) (hour/ns) 60: Performance: 605.662 0.040 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: 0.002 0.001 192.8 60: (ns/day) (hour/ns) 60: Performance: 621.118 0.039 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: 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_secondpart.part0002.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 (25 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: 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: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 197.3 60: (ns/day) (hour/ns) 60: Performance: 642.867 0.037 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: 0.003 0.002 196.1 60: (ns/day) (hour/ns) 60: Performance: 471.382 0.051 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: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.4 60: (ns/day) (hour/ns) 60: Performance: 466.394 0.051 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: 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_secondpart.part0002.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 (26 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: 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: 0.004 0.002 195.3 60: (ns/day) (hour/ns) 60: Performance: 772.585 0.031 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: 0.003 0.001 192.9 60: (ns/day) (hour/ns) 60: Performance: 596.033 0.040 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: 0.003 0.001 193.2 60: (ns/day) (hour/ns) 60: Performance: 579.512 0.041 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: 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_secondpart.part0002.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 (38 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: 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: 0.004 0.002 195.7 60: (ns/day) (hour/ns) 60: Performance: 699.749 0.034 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: 0.003 0.001 193.4 60: (ns/day) (hour/ns) 60: Performance: 547.873 0.044 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: 0.003 0.001 193.3 60: (ns/day) (hour/ns) 60: Performance: 567.314 0.042 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: 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_secondpart.part0002.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 (35 ms) 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (125 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: 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: 0.001 0.001 191.9 60: (ns/day) (hour/ns) 60: Performance: 1991.786 0.012 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: 0.001 0.001 189.5 60: (ns/day) (hour/ns) 60: Performance: 1385.510 0.017 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: 0.001 0.001 190.6 60: (ns/day) (hour/ns) 60: Performance: 1305.641 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.4 60: (ns/day) (hour/ns) 60: Performance: 2065.927 0.012 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: 0.001 0.001 190.0 60: (ns/day) (hour/ns) 60: Performance: 1345.500 0.018 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: 0.001 0.001 189.6 60: (ns/day) (hour/ns) 60: Performance: 1377.319 0.017 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.7 60: (ns/day) (hour/ns) 60: Performance: 2008.671 0.012 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: 0.001 0.001 189.5 60: (ns/day) (hour/ns) 60: Performance: 1390.828 0.017 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: 0.001 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 1344.390 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.002 0.001 195.2 60: (ns/day) (hour/ns) 60: Performance: 1618.228 0.015 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: 0.001 0.001 189.2 60: (ns/day) (hour/ns) 60: Performance: 1052.433 0.023 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: 0.001 0.001 189.1 60: (ns/day) (hour/ns) 60: Performance: 1034.409 0.023 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: 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_secondpart.part0002.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 (10 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: 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: 0.002 0.001 195.2 60: (ns/day) (hour/ns) 60: Performance: 1526.033 0.016 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: 0.001 0.001 193.2 60: (ns/day) (hour/ns) 60: Performance: 1041.677 0.023 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: 0.001 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 996.788 0.024 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: 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_secondpart.part0002.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 (10 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: 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: 0.002 0.001 195.4 60: (ns/day) (hour/ns) 60: Performance: 1443.100 0.017 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: 0.002 0.001 193.3 60: (ns/day) (hour/ns) 60: Performance: 959.827 0.025 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: 0.002 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 924.721 0.026 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: 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_secondpart.part0002.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 (10 ms) 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (60 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: 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: 0.001 0.001 191.1 60: (ns/day) (hour/ns) 60: Performance: 1958.231 0.012 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: 0.001 0.001 189.5 60: (ns/day) (hour/ns) 60: Performance: 1333.398 0.018 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: 0.001 0.001 190.2 60: (ns/day) (hour/ns) 60: Performance: 1272.529 0.019 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.2 60: (ns/day) (hour/ns) 60: Performance: 1957.608 0.012 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: 0.001 0.001 189.0 60: (ns/day) (hour/ns) 60: Performance: 1285.570 0.019 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: 0.001 0.001 189.8 60: (ns/day) (hour/ns) 60: Performance: 1324.732 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.002 0.001 194.9 60: (ns/day) (hour/ns) 60: Performance: 1484.480 0.016 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: 0.002 0.001 194.2 60: (ns/day) (hour/ns) 60: Performance: 999.231 0.024 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: 0.002 0.001 189.1 60: (ns/day) (hour/ns) 60: Performance: 935.329 0.026 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: 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_secondpart.part0002.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 (10 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: 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: 0.002 0.001 194.7 60: (ns/day) (hour/ns) 60: Performance: 1514.031 0.016 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: 0.001 0.001 194.0 60: (ns/day) (hour/ns) 60: Performance: 1012.257 0.024 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: 0.002 0.001 189.6 60: (ns/day) (hour/ns) 60: Performance: 950.595 0.025 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: 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_secondpart.part0002.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 (10 ms) 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (40 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: 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: 0.001 0.001 190.6 60: (ns/day) (hour/ns) 60: Performance: 1988.571 0.012 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: 0.001 0.001 189.2 60: (ns/day) (hour/ns) 60: Performance: 1359.521 0.018 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: 0.001 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 1246.747 0.019 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 2016.561 0.012 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: 0.001 0.001 189.0 60: (ns/day) (hour/ns) 60: Performance: 1291.680 0.019 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: 0.001 0.001 189.3 60: (ns/day) (hour/ns) 60: Performance: 1329.051 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.4 60: (ns/day) (hour/ns) 60: Performance: 1909.669 0.013 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: 0.001 0.001 188.7 60: (ns/day) (hour/ns) 60: Performance: 1353.877 0.018 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: 0.001 0.001 189.2 60: (ns/day) (hour/ns) 60: Performance: 1265.615 0.019 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.4 60: (ns/day) (hour/ns) 60: Performance: 1987.930 0.012 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: 0.001 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 1304.075 0.018 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: 0.001 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 1330.135 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.5 60: (ns/day) (hour/ns) 60: Performance: 1940.344 0.012 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: 0.001 0.001 189.2 60: (ns/day) (hour/ns) 60: Performance: 1356.129 0.018 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: 0.001 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 1280.522 0.019 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 191.7 60: (ns/day) (hour/ns) 60: Performance: 2027.845 0.012 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: 0.001 0.001 189.0 60: (ns/day) (hour/ns) 60: Performance: 1273.025 0.019 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: 0.001 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 1317.774 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 192.0 60: (ns/day) (hour/ns) 60: Performance: 1919.786 0.013 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: 0.001 0.001 188.7 60: (ns/day) (hour/ns) 60: Performance: 1357.258 0.018 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: 0.001 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 1335.582 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.3 60: (ns/day) (hour/ns) 60: Performance: 1988.571 0.012 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: 0.001 0.001 189.0 60: (ns/day) (hour/ns) 60: Performance: 1379.649 0.017 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: 0.001 0.001 189.7 60: (ns/day) (hour/ns) 60: Performance: 1287.600 0.019 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: 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_secondpart.part0002.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 (9 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: 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: 0.001 0.001 191.4 60: (ns/day) (hour/ns) 60: Performance: 2030.519 0.012 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: 0.001 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 1303.553 0.018 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: 0.001 0.001 189.5 60: (ns/day) (hour/ns) 60: Performance: 1292.191 0.019 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: 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_secondpart.part0002.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 (9 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: 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: 0.006 0.003 196.4 60: (ns/day) (hour/ns) 60: Performance: 493.163 0.049 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: 0.003 0.002 194.1 60: (ns/day) (hour/ns) 60: Performance: 436.145 0.055 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 0.002 189.4 60: (ns/day) (hour/ns) 60: Performance: 404.150 0.059 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: 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_secondpart.part0002.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 (19 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: 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: 0.004 0.002 195.3 60: (ns/day) (hour/ns) 60: Performance: 661.150 0.036 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: 0.004 0.002 193.5 60: (ns/day) (hour/ns) 60: Performance: 415.529 0.058 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: 0.003 0.002 188.3 60: (ns/day) (hour/ns) 60: Performance: 443.499 0.054 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: 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_secondpart.part0002.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 (26 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: 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: 0.003 0.002 194.9 60: (ns/day) (hour/ns) 60: Performance: 843.686 0.028 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: 0.003 0.001 193.8 60: (ns/day) (hour/ns) 60: Performance: 555.242 0.043 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: 0.003 0.002 164.0 60: (ns/day) (hour/ns) 60: Performance: 364.575 0.066 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: 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_secondpart.part0002.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 (23 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: 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: 0.003 0.001 195.0 60: (ns/day) (hour/ns) 60: Performance: 989.972 0.024 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: 0.002 0.001 193.0 60: (ns/day) (hour/ns) 60: Performance: 701.245 0.034 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: 0.002 0.001 186.8 60: (ns/day) (hour/ns) 60: Performance: 688.805 0.035 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: 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_secondpart.part0002.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 (18 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: 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: 0.003 0.002 195.5 60: (ns/day) (hour/ns) 60: Performance: 922.797 0.026 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: 0.002 0.001 192.9 60: (ns/day) (hour/ns) 60: Performance: 809.102 0.030 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: 0.002 0.001 187.4 60: (ns/day) (hour/ns) 60: Performance: 724.615 0.033 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: 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_secondpart.part0002.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 (15 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: 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: 0.002 0.001 195.0 60: (ns/day) (hour/ns) 60: Performance: 1214.149 0.020 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: 0.002 0.001 192.8 60: (ns/day) (hour/ns) 60: Performance: 837.783 0.029 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: 0.002 0.001 147.5 60: (ns/day) (hour/ns) 60: Performance: 628.903 0.038 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: 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_secondpart.part0002.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 (13 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: 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: 0.003 0.002 195.8 60: (ns/day) (hour/ns) 60: Performance: 914.306 0.026 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: 0.002 0.001 193.0 60: (ns/day) (hour/ns) 60: Performance: 861.688 0.028 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: 0.002 0.001 188.6 60: (ns/day) (hour/ns) 60: Performance: 814.762 0.029 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: 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_secondpart.part0002.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 (13 ms) 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (219 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: 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: 0.003 0.002 194.8 60: (ns/day) (hour/ns) 60: Performance: 909.850 0.026 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: 0.002 0.001 192.7 60: (ns/day) (hour/ns) 60: Performance: 753.753 0.032 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: 0.002 0.001 187.1 60: (ns/day) (hour/ns) 60: Performance: 724.615 0.033 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: 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_secondpart.part0002.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 (12 ms) 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (12 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: 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: 0.002 0.001 191.9 60: (ns/day) (hour/ns) 60: Performance: 1360.255 0.018 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: 0.001 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 1061.683 0.023 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: 0.001 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 1106.716 0.022 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: 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_secondpart.part0002.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 (12 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: 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: 0.002 0.001 194.1 60: (ns/day) (hour/ns) 60: Performance: 1251.390 0.019 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: 0.002 0.001 193.3 60: (ns/day) (hour/ns) 60: Performance: 830.953 0.029 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: 0.002 0.001 189.3 60: (ns/day) (hour/ns) 60: Performance: 840.807 0.029 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: 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_secondpart.part0002.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 (12 ms) 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (25 ms total) 60: 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: Setting the AWH bias MC random seed to 2063529717 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 -1476405508 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: 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: 0.004 0.002 192.2 60: (ns/day) (hour/ns) 60: Performance: 776.774 0.031 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: 0.003 0.001 189.6 60: (ns/day) (hour/ns) 60: Performance: 564.760 0.042 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: 0.003 0.002 180.1 60: (ns/day) (hour/ns) 60: Performance: 511.366 0.047 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: 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_secondpart.part0002.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 (31 ms) 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: Setting the AWH bias MC random seed to -838999556 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 -36175875 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: 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: 0.004 0.002 193.0 60: (ns/day) (hour/ns) 60: Performance: 730.274 0.033 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: 0.003 0.001 190.0 60: (ns/day) (hour/ns) 60: Performance: 548.334 0.044 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: 0.003 0.002 190.6 60: (ns/day) (hour/ns) 60: Performance: 482.826 0.050 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: 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_secondpart.part0002.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 (31 ms) 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (63 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: 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: Core t (s) Wall t (s) (%) 60: Time: 0.008 0.004 197.7 60: (ns/day) (hour/ns) 60: Performance: 378.880 0.063 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: 0.005 0.002 196.1 60: (ns/day) (hour/ns) 60: Performance: 314.603 0.076 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: 0.005 0.003 191.6 60: (ns/day) (hour/ns) 60: Performance: 296.742 0.081 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: 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_secondpart.part0002.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 (41 ms) 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (41 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: 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 -318772530 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: 0.001 0.000 184.1 60: (ns/day) (hour/ns) 60: Performance: 358.445 0.067 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 (4 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: 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 -312475889 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: 0.001 0.001 191.6 60: (ns/day) (hour/ns) 60: Performance: 265.486 0.090 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 (4 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: 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 -269746699 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: 0.001 0.000 184.4 60: (ns/day) (hour/ns) 60: Performance: 363.296 0.066 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 (4 ms) 60: [----------] 3 tests from Checking/InitialConstraintsTest (12 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 66 tests from 13 test suites ran. (1023 ms total) 60: [ PASSED ] 66 tests. 60/81 Test #60: MdrunIOTests ................................... Passed 1.05 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: 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 1450819064 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: 40 % 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: 0.372 0.186 199.9 61: (ns/day) (hour/ns) 61: Performance: 6.969 3.444 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: 0.251 0.125 199.9 61: (ns/day) (hour/ns) 61: Performance: 10.338 2.322 61: [ OK ] CompelTest.SwapCanRun (693 ms) 61: [----------] 1 test from CompelTest (693 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: 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: 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: 0.000 0.000 187.5 61: (ns/day) (hour/ns) 61: Performance: 514.755 0.047 61: Setting the LD random seed to 2144321238 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 (3 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: 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: 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: 0.000 0.000 185.5 61: (ns/day) (hour/ns) 61: Performance: 535.285 0.045 61: Setting the LD random seed to 2139078390 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 (3 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: 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: 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: 0.000 0.000 186.3 61: (ns/day) (hour/ns) 61: Performance: 540.877 0.044 61: Setting the LD random seed to 2013132727 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 (3 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: 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: 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: 0.000 0.000 186.8 61: (ns/day) (hour/ns) 61: Performance: 581.682 0.041 61: Setting the LD random seed to -359665697 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 (3 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: 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: 14 % 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: 0.000 0.000 170.8 61: (ns/day) (hour/ns) 61: Performance: 498.470 0.048 61: Setting the LD random seed to 2113294287 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 (3 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: 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: 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: 0.000 0.000 187.2 61: (ns/day) (hour/ns) 61: Performance: 563.589 0.043 61: Setting the LD random seed to -872768689 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 (3 ms) 61: [----------] 6 tests from BondedInteractionsTest (20 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: 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 2133163511 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: 0.007 0.004 197.6 61: (ns/day) (hour/ns) 61: Performance: 118.427 0.203 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: 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 2146846578 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: 0.005 0.003 196.4 61: (ns/day) (hour/ns) 61: Performance: 166.355 0.144 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (33 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: 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 769629421 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: 0.007 0.004 197.4 61: (ns/day) (hour/ns) 61: Performance: 122.528 0.196 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: 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 -84021803 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: 0.005 0.003 196.3 61: (ns/day) (hour/ns) 61: Performance: 165.429 0.145 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (29 ms) 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (62 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: 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 -1078018053 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: 0.001 0.001 186.9 61: (ns/day) (hour/ns) 61: Performance: 721.601 0.033 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: 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 -203427857 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: 0.001 0.001 188.1 61: (ns/day) (hour/ns) 61: Performance: 660.087 0.036 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (8 ms) 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (9 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: 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: 0.002 0.001 191.2 61: (ns/day) (hour/ns) 61: Performance: 842.762 0.028 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (9 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: 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: 0.002 0.001 190.8 61: (ns/day) (hour/ns) 61: Performance: 851.342 0.028 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (9 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: 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: 0.002 0.001 191.0 61: (ns/day) (hour/ns) 61: Performance: 773.232 0.031 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (9 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: 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: 0.002 0.001 192.4 61: (ns/day) (hour/ns) 61: Performance: 791.048 0.030 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (10 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: 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: 0.002 0.001 191.9 61: (ns/day) (hour/ns) 61: Performance: 793.164 0.030 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (10 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: 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: 0.002 0.001 191.6 61: (ns/day) (hour/ns) 61: Performance: 857.836 0.028 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (12 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: 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: 0.002 0.001 191.4 61: (ns/day) (hour/ns) 61: Performance: 857.159 0.028 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (11 ms) 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest (74 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: 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 -11551789 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: 0.001 0.001 187.2 61: (ns/day) (hour/ns) 61: Performance: 2873.560 0.008 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (4 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: 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 -12734543 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: 0.001 0.001 187.4 61: (ns/day) (hour/ns) 61: Performance: 2910.746 0.008 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (3 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: 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 -272964108 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: 0.001 0.001 189.5 61: (ns/day) (hour/ns) 61: Performance: 2609.193 0.009 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (3 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: 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 -1275626245 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: 0.001 0.001 189.1 61: (ns/day) (hour/ns) 61: Performance: 2603.985 0.009 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (3 ms) 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (15 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 22 tests from 6 test suites ran. (925 ms total) 61: [ PASSED ] 21 tests. 61: [ SKIPPED ] 1 test, listed below: 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61/81 Test #61: MdrunTestsOneRank .............................. Passed 0.95 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: 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 -12636165 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: 10.3%. 62: The balanceable part of the MD step is 23%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 2.4%. 62: 62: 62: NOTE: 5 % 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: 0.675 0.169 399.8 62: (ns/day) (hour/ns) 62: Performance: 7.672 3.128 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: 22 % 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: 0.483 0.121 399.5 62: (ns/day) (hour/ns) 62: Performance: 10.726 2.237 62: [ OK ] CompelTest.SwapCanRun (696 ms) 62: [----------] 1 test from CompelTest (696 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: 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: 17 % 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: 0.001 0.000 376.8 62: (ns/day) (hour/ns) 62: Performance: 291.426 0.082 62: Setting the LD random seed to 1327300510 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 (4 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: 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: NOTE: 19 % 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: 0.001 0.000 376.4 62: (ns/day) (hour/ns) 62: Performance: 330.797 0.073 62: Setting the LD random seed to 752150487 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 (5 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: 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: 11 % 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: Core t (s) Wall t (s) (%) 62: Time: 0.002 0.000 381.8 62: (ns/day) (hour/ns) 62: Performance: 203.818 0.118 62: Setting the LD random seed to -1107902473 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 (5 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: 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: 19 % 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: 0.001 0.000 377.9 62: (ns/day) (hour/ns) 62: Performance: 328.101 0.073 62: Setting the LD random seed to 1588518827 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 (5 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: 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: 17 % 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: 0.001 0.000 377.4 62: (ns/day) (hour/ns) 62: Performance: 362.388 0.066 62: Setting the LD random seed to -671115026 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 (4 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: 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: 18 % 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: 0.001 0.000 376.6 62: (ns/day) (hour/ns) 62: Performance: 320.839 0.075 62: Setting the LD random seed to -327155841 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 (6 ms) 62: [----------] 6 tests from BondedInteractionsTest (31 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: 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 920255933 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: 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: 0.011 0.003 391.4 62: (ns/day) (hour/ns) 62: Performance: 159.270 0.151 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: 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 1602222079 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: 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: 0.008 0.002 389.8 62: (ns/day) (hour/ns) 62: Performance: 200.026 0.120 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (43 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: 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 -680798251 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: 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: 0.011 0.003 391.3 62: (ns/day) (hour/ns) 62: Performance: 157.656 0.152 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: 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 -37782193 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: 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: 0.008 0.002 389.1 62: (ns/day) (hour/ns) 62: Performance: 199.586 0.120 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (38 ms) 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (82 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: 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 2104479598 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: 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: 0.003 0.001 373.5 62: (ns/day) (hour/ns) 62: Performance: 533.944 0.045 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: 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 -35799041 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: 33 % 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: 0.005 0.001 368.6 62: (ns/day) (hour/ns) 62: Performance: 301.037 0.080 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (18 ms) 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (18 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: 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 48%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 13.0%. 62: 62: NOTE: 13.0 % 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: 21 % 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 0.002 370.8 62: (ns/day) (hour/ns) 62: Performance: 407.152 0.059 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (23 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: 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: 25.4%. 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: 12.2%. 62: 62: NOTE: 12.2 % 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: 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 0.002 383.1 62: (ns/day) (hour/ns) 62: Performance: 353.741 0.068 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (20 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: 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: 27.0%. 62: The balanceable part of the MD step is 52%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 14.0%. 62: 62: NOTE: 14.0 % 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: 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: 0.008 0.002 385.2 62: (ns/day) (hour/ns) 62: Performance: 378.012 0.063 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (19 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: 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: 31 % 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 0.002 393.0 62: (ns/day) (hour/ns) 62: Performance: 338.592 0.071 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (19 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: 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: 21 % 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: 0.005 0.001 384.2 62: (ns/day) (hour/ns) 62: Performance: 552.374 0.043 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (16 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: 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: 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: 0.005 0.001 385.0 62: (ns/day) (hour/ns) 62: Performance: 602.307 0.040 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (18 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: 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: 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: 0.005 0.001 380.6 62: (ns/day) (hour/ns) 62: Performance: 600.643 0.040 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (18 ms) 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest (138 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: 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 -135334041 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 50%, 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: 28 % 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: 0.005 0.001 371.6 62: (ns/day) (hour/ns) 62: Performance: 1092.535 0.022 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (11 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: 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 1979185520 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: 0.1%. 62: The balanceable part of the MD step is 50%, 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: 28 % 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: 0.005 0.001 370.4 62: (ns/day) (hour/ns) 62: Performance: 1114.468 0.022 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (11 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: 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 -404005987 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: 0.5%. 62: The balanceable part of the MD step is 54%, 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: 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: 0.005 0.001 372.2 62: (ns/day) (hour/ns) 62: Performance: 1088.888 0.022 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (11 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: 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 1728052667 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: 0.4%. 62: The balanceable part of the MD step is 56%, 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: 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: 0.005 0.001 374.2 62: (ns/day) (hour/ns) 62: Performance: 1061.597 0.023 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (11 ms) 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (45 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 22 tests from 6 test suites ran. (1078 ms total) 62: [ PASSED ] 21 tests. 62: [ SKIPPED ] 1 test, listed below: 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62/81 Test #62: MdrunTestsTwoRanks ............................. Passed 1.11 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: 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 -135235 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: 0.011 0.005 198.2 63: (ns/day) (hour/ns) 63: Performance: 358.316 0.067 63: [ OK ] OriresTest.OriresCanRun (142 ms) 63: [----------] 1 test from OriresTest (142 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: 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 -1929948771 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: 0.029 0.015 199.4 63: (ns/day) (hour/ns) 63: Performance: 312.173 0.077 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 (26 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: 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 -308480041 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: 0.014 0.007 198.8 63: (ns/day) (hour/ns) 63: Performance: 659.527 0.036 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 (14 ms) 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (40 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 4 tests from 2 test suites ran. (205 ms total) 63: [ PASSED ] 4 tests. 63/81 Test #63: MdrunSingleRankAlgorithmsTests ................. Passed 0.22 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 0.420 0.4198 2.5241 1.5001 64: [ OK ] NonbondedBenchTest.BasicEndToEndTest (58 ms) 64: [----------] 1 test from NonbondedBenchTest (58 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: 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 = -4.79910463671092e+01 64: Maximum force = 1.86297359432231e+02 on atom 13 64: Norm of force = 8.77219865482157e+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 (253 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: 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 = -5.58622538633302e+01 64: Maximum force = 4.27274822366368e+02 on atom 13 64: Norm of force = 1.84530029253754e+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 (261 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: 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 = 3.19376899751523e+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 (61 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: 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 = 1.51743018140928e+02 64: Maximum force = 7.42089573409108e+03 on atom 9 64: Norm of force = 3.56929298615740e+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 (61 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: 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 = 4.56923624626570e+02 on atom 17 64: Norm of force = 1.83258377168389e+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 (9 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: 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 = -1.69410778678181e+02 64: Maximum force = 2.18225948473987e+02 on atom 17 64: Norm of force = 7.92068036537548e+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 (9 ms) 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (657 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: 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 (3 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: 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 = -9.90642313893957e-01 64: Maximum force = 2.57812909491105e+00 on atom 1 64: Norm of force = 1.05251679559258e+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 (3 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: 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 = -9.90642313893957e-01 64: Maximum force = 2.57812909491105e+00 on atom 1 64: Norm of force = 1.05251679559258e+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 (3 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: 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 = 3.19395484891520e+02 64: Maximum force = 9.97041707197911e+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 (61 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: 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 = 7.50181017480397e+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 (61 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: 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 = 5.61116097794205e+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 (62 ms) 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (196 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: 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 (6 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: 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 (780 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: 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 (263 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: 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 (265 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: 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 (4 ms) 64: [----------] 5 tests from NormalModesWorks/NormalModesTest (1321 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: 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: 0.001 0.001 192.0 64: (ns/day) (hour/ns) 64: Performance: 1920.983 0.012 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: 20 % 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 0.000 193.2 64: (ns/day) (hour/ns) 64: Performance: 4332.344 0.006 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.002 0.001 195.3 64: (ns/day) (hour/ns) 64: Performance: 1546.722 0.016 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: 19 % 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 0.000 192.8 64: (ns/day) (hour/ns) 64: Performance: 4005.588 0.006 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.001 0.001 192.5 64: (ns/day) (hour/ns) 64: Performance: 2029.850 0.012 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: 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 0.000 193.0 64: (ns/day) (hour/ns) 64: Performance: 4378.531 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (5 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: 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: 0.001 0.001 193.3 64: (ns/day) (hour/ns) 64: Performance: 2098.295 0.011 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: 19 % 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 0.000 193.3 64: (ns/day) (hour/ns) 64: Performance: 4228.273 0.006 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (5 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: 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: 0.005 0.002 196.3 64: (ns/day) (hour/ns) 64: Performance: 627.991 0.038 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: 29 % 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 0.000 193.2 64: (ns/day) (hour/ns) 64: Performance: 3330.051 0.007 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (268 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: 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: 0.005 0.002 197.4 64: (ns/day) (hour/ns) 64: Performance: 621.028 0.039 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: 26 % 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 0.000 193.0 64: (ns/day) (hour/ns) 64: Performance: 3606.905 0.007 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (268 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: 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: 0.004 0.002 196.4 64: (ns/day) (hour/ns) 64: Performance: 713.941 0.034 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: 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 0.000 193.3 64: (ns/day) (hour/ns) 64: Performance: 3514.315 0.007 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (267 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: 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: 0.005 0.002 196.5 64: (ns/day) (hour/ns) 64: Performance: 629.853 0.038 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: 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: 0.001 0.000 193.8 64: (ns/day) (hour/ns) 64: Performance: 3540.571 0.007 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (267 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: 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: 0.004 0.002 195.2 64: (ns/day) (hour/ns) 64: Performance: 762.261 0.031 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: 18 % 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 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 2125.075 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 195.8 64: (ns/day) (hour/ns) 64: Performance: 700.227 0.034 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: 18 % 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 0.001 194.7 64: (ns/day) (hour/ns) 64: Performance: 2117.043 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 195.9 64: (ns/day) (hour/ns) 64: Performance: 774.041 0.031 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: 18 % 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 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 2076.371 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (22 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: 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: 0.005 0.002 196.6 64: (ns/day) (hour/ns) 64: Performance: 594.078 0.040 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: 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: 0.001 0.001 194.1 64: (ns/day) (hour/ns) 64: Performance: 2050.797 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 ms) 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (1166 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: 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: 0.004 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 787.699 0.030 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: 0.002 0.001 194.1 64: (ns/day) (hour/ns) 64: Performance: 1646.777 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 194.6 64: (ns/day) (hour/ns) 64: Performance: 811.352 0.030 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: 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: 0.002 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 1668.633 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 194.4 64: (ns/day) (hour/ns) 64: Performance: 800.701 0.030 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: 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: 0.002 0.001 194.0 64: (ns/day) (hour/ns) 64: Performance: 1699.943 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 805.622 0.030 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: 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: 0.002 0.001 194.2 64: (ns/day) (hour/ns) 64: Performance: 1674.985 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 194.4 64: (ns/day) (hour/ns) 64: Performance: 814.786 0.029 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: 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: 0.002 0.001 193.8 64: (ns/day) (hour/ns) 64: Performance: 1631.945 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.005 0.002 195.6 64: (ns/day) (hour/ns) 64: Performance: 601.620 0.040 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: 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: 0.002 0.001 193.6 64: (ns/day) (hour/ns) 64: Performance: 1624.201 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 795.428 0.030 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: 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: 0.002 0.001 193.6 64: (ns/day) (hour/ns) 64: Performance: 1660.090 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 811.566 0.030 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: 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 0.001 193.5 64: (ns/day) (hour/ns) 64: Performance: 1656.964 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 794.915 0.030 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: 0.002 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 1646.337 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.003 0.002 194.4 64: (ns/day) (hour/ns) 64: Performance: 816.730 0.029 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: 0.002 0.001 193.5 64: (ns/day) (hour/ns) 64: Performance: 1719.395 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 800.285 0.030 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: 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: 0.002 0.001 193.3 64: (ns/day) (hour/ns) 64: Performance: 1643.263 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.005 0.002 197.1 64: (ns/day) (hour/ns) 64: Performance: 643.404 0.037 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: 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: 0.002 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 1664.575 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 197.2 64: (ns/day) (hour/ns) 64: Performance: 656.150 0.037 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: 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: 0.002 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 1693.401 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 197.1 64: (ns/day) (hour/ns) 64: Performance: 650.675 0.037 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: 0.002 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1642.825 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.005 0.002 197.1 64: (ns/day) (hour/ns) 64: Performance: 634.655 0.038 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: 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: 0.002 0.001 193.6 64: (ns/day) (hour/ns) 64: Performance: 1635.411 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 197.0 64: (ns/day) (hour/ns) 64: Performance: 649.441 0.037 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: 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: 0.002 0.001 193.7 64: (ns/day) (hour/ns) 64: Performance: 1686.910 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 196.8 64: (ns/day) (hour/ns) 64: Performance: 646.781 0.037 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: 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: 0.002 0.001 193.8 64: (ns/day) (hour/ns) 64: Performance: 1680.009 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (15 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: 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: 0.004 0.002 197.1 64: (ns/day) (hour/ns) 64: Performance: 653.921 0.037 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: 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: 0.002 0.001 194.2 64: (ns/day) (hour/ns) 64: Performance: 1634.543 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 197.0 64: (ns/day) (hour/ns) 64: Performance: 643.606 0.037 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: 0.002 0.001 193.5 64: (ns/day) (hour/ns) 64: Performance: 1638.020 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 197.3 64: (ns/day) (hour/ns) 64: Performance: 662.857 0.036 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: 0.002 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 1699.005 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 197.1 64: (ns/day) (hour/ns) 64: Performance: 658.746 0.036 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: 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: 0.002 0.001 193.8 64: (ns/day) (hour/ns) 64: Performance: 1648.540 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 197.0 64: (ns/day) (hour/ns) 64: Performance: 649.441 0.037 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: 0.002 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 1651.191 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 195.2 64: (ns/day) (hour/ns) 64: Performance: 740.634 0.032 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: 0.002 0.001 194.0 64: (ns/day) (hour/ns) 64: Performance: 1581.667 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 195.2 64: (ns/day) (hour/ns) 64: Performance: 724.605 0.033 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: 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: 0.002 0.001 193.6 64: (ns/day) (hour/ns) 64: Performance: 1633.676 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 195.3 64: (ns/day) (hour/ns) 64: Performance: 729.755 0.033 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: 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: 0.002 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 1629.787 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 195.2 64: (ns/day) (hour/ns) 64: Performance: 728.806 0.033 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: 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: 0.002 0.001 194.0 64: (ns/day) (hour/ns) 64: Performance: 1592.296 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 740.367 0.032 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: 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: 0.002 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 1568.379 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (21 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: 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: 0.004 0.002 195.6 64: (ns/day) (hour/ns) 64: Performance: 732.184 0.033 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: 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: 0.002 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1612.299 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 195.4 64: (ns/day) (hour/ns) 64: Performance: 727.944 0.033 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: 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: 0.002 0.001 193.8 64: (ns/day) (hour/ns) 64: Performance: 1643.702 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 195.3 64: (ns/day) (hour/ns) 64: Performance: 726.999 0.033 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: 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: 0.002 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1602.652 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (21 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: 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: 0.004 0.002 195.4 64: (ns/day) (hour/ns) 64: Performance: 741.615 0.032 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: 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: 0.002 0.001 194.0 64: (ns/day) (hour/ns) 64: Performance: 1560.829 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 195.5 64: (ns/day) (hour/ns) 64: Performance: 726.656 0.033 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: 0.002 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 1642.825 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 195.4 64: (ns/day) (hour/ns) 64: Performance: 721.719 0.033 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: 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: 0.002 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1652.077 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (21 ms) 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (553 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: 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: 0.003 0.001 195.2 64: (ns/day) (hour/ns) 64: Performance: 3075.683 0.008 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 (5 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: 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: 0.003 0.002 197.0 64: (ns/day) (hour/ns) 64: Performance: 2647.061 0.009 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 (5 ms) 64: [----------] 2 tests from Angles1/SimpleMdrunTest (11 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 65 tests from 7 test suites ran. (4008 ms total) 64: [ PASSED ] 65 tests. 64/81 Test #64: MdrunNonIntegratorTests ........................ Passed 4.04 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: 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 (289 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: 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 (249 ms) 65: [----------] 2 tests from Simple/TpiTest (539 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 2 tests from 1 test suite ran. (545 ms total) 65: [ PASSED ] 2 tests. 65/81 Test #65: MdrunTpiTests .................................. Passed 0.56 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: 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: 21 % 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: NOTE: 7 % 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: 0.001 0.000 318.9 66: (ns/day) (hour/ns) 66: Performance: 353.377 0.068 66: Setting the LD random seed to -9442453 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 (5 ms) 66: [----------] 1 test from DomainDecompositionSpecialCasesTest (5 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: 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: 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: 0.001 0.000 377.9 66: (ns/day) (hour/ns) 66: Performance: 327.804 0.073 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 -1154502705 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 (4 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: 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: 21 % of the run time was spent in domain decomposition, 66: 13 % 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: 0.001 0.000 364.1 66: (ns/day) (hour/ns) 66: Performance: 317.327 0.076 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 -839919685 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 (4 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: 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: 18 % 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: 10 % 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: 0.001 0.000 380.8 66: (ns/day) (hour/ns) 66: Performance: 291.895 0.082 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 -563118145 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 (4 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: 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: NOTE: 16 % 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: 0.002 0.000 385.8 66: (ns/day) (hour/ns) 66: Performance: 178.340 0.135 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 1869805181 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 (13 ms) 66: [----------] 4 tests from MimicTest (27 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: 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 = -4.79910463671093e+01 66: Maximum force = 1.86297359432232e+02 on atom 13 66: Norm of force = 8.77219865482159e+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 (311 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: 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 = -5.58622538633302e+01 66: Maximum force = 4.27274822366366e+02 on atom 13 66: Norm of force = 1.84530029253753e+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 (265 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: 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 = 3.19376899751523e+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 (68 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: 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 = 7.42089573409111e+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 (63 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: 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 = -1.56984193848275e+02 66: Maximum force = 4.56923624626570e+02 on atom 17 66: Norm of force = 1.83258377168389e+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 (10 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: 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 = -1.69410778678181e+02 66: Maximum force = 2.18225948473987e+02 on atom 17 66: Norm of force = 7.92068036537548e+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 (11 ms) 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (732 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: 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 (4 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: 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 = -9.90642313893957e-01 66: Maximum force = 2.57812909491105e+00 on atom 3 66: Norm of force = 1.05251679559258e+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 (4 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 (2 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: 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 = 3.19395484891520e+02 66: Maximum force = 9.97041707197911e+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 (62 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: 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 (62 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 (57 ms) 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (194 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 17 tests from 4 test suites ran. (987 ms total) 66: [ PASSED ] 17 tests. 66/81 Test #66: MdrunMpiTests .................................. Passed 1.00 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. (14 ms total) 67: [ PASSED ] 2 tests. 67: 67: YOU HAVE 4 DISABLED TESTS 67: 67/81 Test #67: MdrunMultiSimTests ............................. Passed 0.03 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. (14 ms total) 68: [ PASSED ] 1 test. 68: 68: YOU HAVE 4 DISABLED TESTS 68: 68/81 Test #68: MdrunMultiSimReplexTests ....................... Passed 0.03 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 0.02 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 -100802641 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 -612507651 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: 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: 0.046 0.023 199.5 70: (ns/day) (hour/ns) 70: Performance: 77.974 0.308 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 (34 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 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: 0.045 0.023 199.6 70: (ns/day) (hour/ns) 70: Performance: 80.100 0.300 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 (28 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: 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: 0.009 0.004 197.0 70: (ns/day) (hour/ns) 70: Performance: 20.005 1.200 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 (18 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: 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: 0.043 0.022 199.6 70: (ns/day) (hour/ns) 70: Performance: 83.747 0.287 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 (27 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 (109 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 19 tests from 1 test suite ran. (134 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 0.15 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 132048895 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 -1446433 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: 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: 10.4%. 71: The balanceable part of the MD step is 9%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.9%. 71: 71: 71: NOTE: 8 % 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: 0.066 0.017 397.9 71: (ns/day) (hour/ns) 71: Performance: 109.274 0.220 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 (34 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 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: 9.2%. 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: 0.7%. 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.062 0.016 397.7 71: (ns/day) (hour/ns) 71: Performance: 115.871 0.207 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 (26 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: 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: 0.010 0.003 384.5 71: (ns/day) (hour/ns) 71: Performance: 32.752 0.733 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 (22 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: 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: 0.086 0.021 399.1 71: (ns/day) (hour/ns) 71: Performance: 84.547 0.284 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 (30 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 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: 0.083 0.021 399.2 71: (ns/day) (hour/ns) 71: Performance: 86.955 0.276 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 (27 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: 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: 0.019 0.005 395.7 71: (ns/day) (hour/ns) 71: Performance: 18.089 1.327 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 (26 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: 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: 13.8%. 71: The balanceable part of the MD step is 7%, 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: 0.059 0.015 398.5 71: (ns/day) (hour/ns) 71: Performance: 122.566 0.196 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 (23 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 (193 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 19 tests from 1 test suite ran. (219 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 0.24 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: 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: 0.003 0.003 98.2 72: (ns/day) (hour/ns) 72: Performance: 469.916 0.051 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: 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 97.0 72: (ns/day) (hour/ns) 72: Performance: 936.118 0.026 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: 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: 0.001 0.001 95.5 72: (ns/day) (hour/ns) 72: Performance: 1507.732 0.016 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: 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: 0.001 0.001 95.2 72: (ns/day) (hour/ns) 72: Performance: 1692.936 0.014 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: 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 97.4 72: (ns/day) (hour/ns) 72: Performance: 887.822 0.027 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: 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: 0.001 0.001 95.4 72: (ns/day) (hour/ns) 72: Performance: 1824.820 0.013 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 (45 ms) 72: [----------] 1 test from BasicPropagators/PeriodicActionsTest (45 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 1 test from 1 test suite ran. (59 ms total) 72: [ PASSED ] 1 test. 72/81 Test #72: MdrunMpiCoordinationBasicTestsOneRank .......... Passed 0.08 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: 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: 0.6%. 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: 0.4%. 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: 0.007 0.004 195.5 73: (ns/day) (hour/ns) 73: Performance: 393.397 0.061 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: 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: 0.3%. 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: 24 % 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 0.002 191.4 73: (ns/day) (hour/ns) 73: Performance: 785.790 0.031 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: 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: 1.4%. 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: 0.8%. 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: 0.003 0.002 190.0 73: (ns/day) (hour/ns) 73: Performance: 862.466 0.028 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: 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: 2.5%. 73: The balanceable part of the MD step is 26%, 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: 37 % 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 0.003 193.6 73: (ns/day) (hour/ns) 73: Performance: 585.469 0.041 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: 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 55%, 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: 0.003 0.002 189.8 73: (ns/day) (hour/ns) 73: Performance: 976.322 0.025 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: 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 turned on during the run due to measured imbalance. 73: Average load imbalance: 6.5%. 73: The balanceable part of the MD step is 57%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 3.7%. 73: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 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: 0.003 0.001 191.0 73: (ns/day) (hour/ns) 73: Performance: 1057.613 0.023 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 (64 ms) 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest (64 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (79 ms total) 73: [ PASSED ] 1 test. 73/81 Test #73: MdrunMpiCoordinationBasicTestsTwoRanks ......... Passed 0.10 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: 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: 0.003 0.003 97.9 74: (ns/day) (hour/ns) 74: Performance: 431.989 0.056 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 1090.757 0.022 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1085.758 0.022 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: 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: 0.001 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 1609.351 0.015 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 1669.085 0.014 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1258.034 0.019 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 (49 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1273.903 0.019 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1374.826 0.017 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2125.809 0.011 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2051.480 0.012 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2000.842 0.012 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: 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: 0.001 0.001 92.6 74: (ns/day) (hour/ns) 74: Performance: 2201.785 0.011 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 (32 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1608.090 0.015 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: 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: 0.001 0.001 95.5 74: (ns/day) (hour/ns) 74: Performance: 2044.671 0.012 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2533.139 0.009 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: 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: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 1496.379 0.016 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2336.213 0.010 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: 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 1552.960 0.015 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 (27 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1861.769 0.013 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: 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: 0.001 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 2290.184 0.010 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2665.770 0.009 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: 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: 0.001 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2562.643 0.009 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: 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: 0.001 0.001 95.3 74: (ns/day) (hour/ns) 74: Performance: 2503.289 0.010 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2449.540 0.010 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 (23 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: 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 1775.387 0.014 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: 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: 0.001 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 2210.475 0.011 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2566.914 0.009 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2385.977 0.010 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2435.017 0.010 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2506.344 0.010 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 (23 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: 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: 0.001 0.001 94.3 74: (ns/day) (hour/ns) 74: Performance: 1784.128 0.013 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: 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: 0.001 0.001 95.8 74: (ns/day) (hour/ns) 74: Performance: 2283.393 0.011 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2704.387 0.009 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2493.158 0.010 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2514.528 0.010 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2527.942 0.009 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 (23 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1845.594 0.013 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2219.234 0.011 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2651.999 0.009 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2482.109 0.010 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2448.567 0.010 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2458.337 0.010 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 (24 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: 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 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1897.319 0.013 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: 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 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 2368.548 0.010 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: 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: 0.000 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2801.543 0.009 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: 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 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2593.934 0.009 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: 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 0.001 95.3 74: (ns/day) (hour/ns) 74: Performance: 2588.485 0.009 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2550.970 0.009 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 (23 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 1800.290 0.013 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: 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: 0.001 0.001 95.4 74: (ns/day) (hour/ns) 74: Performance: 2245.114 0.011 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2668.079 0.009 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: 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: 0.001 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2524.833 0.010 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2492.150 0.010 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2542.548 0.009 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 (24 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 1841.732 0.013 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: 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: 0.001 0.001 95.6 74: (ns/day) (hour/ns) 74: Performance: 2245.114 0.011 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2687.868 0.009 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2507.364 0.010 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2504.306 0.010 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2554.143 0.009 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 (23 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 1826.443 0.013 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: 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: 0.001 0.001 95.4 74: (ns/day) (hour/ns) 74: Performance: 2268.260 0.011 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2753.953 0.009 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2459.319 0.010 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2528.979 0.009 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2537.312 0.009 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 (23 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: 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 97.1 74: (ns/day) (hour/ns) 74: Performance: 1859.521 0.013 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: 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 96.3 74: (ns/day) (hour/ns) 74: Performance: 2324.752 0.010 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: 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 95.8 74: (ns/day) (hour/ns) 74: Performance: 2772.544 0.009 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: 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 96.1 74: (ns/day) (hour/ns) 74: Performance: 2442.741 0.010 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: 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 96.1 74: (ns/day) (hour/ns) 74: Performance: 2414.026 0.010 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: 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 96.8 74: (ns/day) (hour/ns) 74: Performance: 1893.819 0.013 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 (23 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: 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: 0.001 0.001 97.0 74: (ns/day) (hour/ns) 74: Performance: 1786.197 0.013 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: 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 2088.337 0.011 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: 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: 0.001 0.001 96.0 74: (ns/day) (hour/ns) 74: Performance: 2492.150 0.010 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 2325.630 0.010 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 2348.682 0.010 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: 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: 0.001 0.001 96.0 74: (ns/day) (hour/ns) 74: Performance: 2470.166 0.010 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 (23 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1748.182 0.014 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 2179.198 0.011 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: 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: 0.001 0.001 95.5 74: (ns/day) (hour/ns) 74: Performance: 2583.058 0.009 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: 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: 0.001 0.001 95.8 74: (ns/day) (hour/ns) 74: Performance: 2344.214 0.010 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 2390.607 0.010 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: 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: 0.001 0.001 95.8 74: (ns/day) (hour/ns) 74: Performance: 2417.815 0.010 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 (23 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: 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: 0.001 0.001 97.9 74: (ns/day) (hour/ns) 74: Performance: 1534.012 0.016 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: 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: 0.001 0.001 97.6 74: (ns/day) (hour/ns) 74: Performance: 1790.870 0.013 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: 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: 0.001 0.001 97.3 74: (ns/day) (hour/ns) 74: Performance: 2009.326 0.012 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1909.078 0.013 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: 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: 0.001 0.001 97.4 74: (ns/day) (hour/ns) 74: Performance: 1919.188 0.013 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1879.949 0.013 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 (23 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: 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: 0.001 0.001 97.9 74: (ns/day) (hour/ns) 74: Performance: 1453.656 0.017 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: 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: 0.001 0.001 97.3 74: (ns/day) (hour/ns) 74: Performance: 1693.401 0.014 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1958.231 0.012 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: 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: 0.001 0.001 97.0 74: (ns/day) (hour/ns) 74: Performance: 1741.264 0.014 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: 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: 0.001 0.001 97.3 74: (ns/day) (hour/ns) 74: Performance: 1801.870 0.013 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: 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: 0.001 0.001 97.7 74: (ns/day) (hour/ns) 74: Performance: 1237.067 0.019 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 (24 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1510.320 0.016 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1724.690 0.014 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: 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: 0.001 0.001 96.0 74: (ns/day) (hour/ns) 74: Performance: 2021.192 0.012 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1767.746 0.014 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1845.042 0.013 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1878.230 0.013 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 (24 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1448.870 0.017 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 1709.377 0.014 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: 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: 0.001 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 1878.230 0.013 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: 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: 0.001 0.001 96.0 74: (ns/day) (hour/ns) 74: Performance: 1760.170 0.014 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1771.813 0.014 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1774.365 0.014 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 (25 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1470.660 0.016 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 1712.703 0.014 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: 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: 0.001 0.001 96.0 74: (ns/day) (hour/ns) 74: Performance: 1846.701 0.013 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: 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: 0.001 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 1692.471 0.014 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1785.162 0.013 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: 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: 0.001 0.001 95.6 74: (ns/day) (hour/ns) 74: Performance: 1720.356 0.014 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 (25 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: 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: 0.001 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1292.071 0.019 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: 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: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 1461.241 0.016 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1651.634 0.015 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: 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: 0.001 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1552.569 0.015 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1572.784 0.015 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1578.425 0.015 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 (26 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1056.343 0.023 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 1179.964 0.020 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1256.751 0.019 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: 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: 0.001 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1213.193 0.020 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1184.730 0.020 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: 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: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 1202.302 0.020 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 (27 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1266.569 0.019 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1468.556 0.016 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1622.063 0.015 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1532.105 0.016 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1506.626 0.016 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1489.865 0.016 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 (25 ms) 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (572 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 22 tests from 1 test suite ran. (587 ms total) 74: [ PASSED ] 22 tests. 74/81 Test #74: MdrunMpiCoordinationCouplingTestsOneRank ....... Passed 0.61 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: 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: 4.5%. 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: 2.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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: 0.007 0.004 195.1 75: (ns/day) (hour/ns) 75: Performance: 392.607 0.061 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: 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: 7.2%. 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: 4.1%. 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: 0.003 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 810.338 0.030 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: 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: 2.3%. 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: 1.2%. 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: 0.003 0.001 188.7 75: (ns/day) (hour/ns) 75: Performance: 999.447 0.024 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: 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: 3.2%. 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: 1.7%. 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: 0.003 0.001 188.9 75: (ns/day) (hour/ns) 75: Performance: 991.964 0.024 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: 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: 6.7%. 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: 3.5%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 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 0.002 192.2 75: (ns/day) (hour/ns) 75: Performance: 797.953 0.030 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: 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: 7.2%. 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: 3.7%. 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: 0.003 0.001 190.4 75: (ns/day) (hour/ns) 75: Performance: 1083.372 0.022 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 (62 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: 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: 3.5%. 75: The balanceable part of the MD step is 50%, 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: 21 % of the run time was 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: 782.298 0.031 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: 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: 4.8%. 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: 2.8%. 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: 0.003 0.001 191.0 75: (ns/day) (hour/ns) 75: Performance: 1068.991 0.022 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: 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: 7.8%. 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: 4.3%. 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: 0.002 0.001 190.3 75: (ns/day) (hour/ns) 75: Performance: 1311.044 0.018 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: 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: 12.5%. 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: 6.5%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.5 % 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: 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: 0.002 0.001 190.7 75: (ns/day) (hour/ns) 75: Performance: 1151.298 0.021 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: 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: 9.3%. 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: 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: 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: 0.002 0.001 190.2 75: (ns/day) (hour/ns) 75: Performance: 1224.283 0.020 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: 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: 9.6%. 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: 5.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.2 % 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: 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: 0.002 0.001 190.1 75: (ns/day) (hour/ns) 75: Performance: 1220.040 0.020 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 (42 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: 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: 3.6%. 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: 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: 0.003 0.002 192.4 75: (ns/day) (hour/ns) 75: Performance: 933.706 0.026 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: 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: 10.0%. 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: 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: 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: 0.003 0.001 191.7 75: (ns/day) (hour/ns) 75: Performance: 1070.105 0.022 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: 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: 9.4%. 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: 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: 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: 0.002 0.001 190.7 75: (ns/day) (hour/ns) 75: Performance: 1397.594 0.017 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: 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: 11.7%. 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: 6.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.2 % 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: 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: 0.002 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1277.601 0.019 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: 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: 10.7%. 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: 5.6%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.6 % 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: 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: 0.002 0.001 190.6 75: (ns/day) (hour/ns) 75: Performance: 1358.455 0.018 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: 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: 13.5%. 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: 7.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 7.2 % 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: 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: 0.002 0.001 191.1 75: (ns/day) (hour/ns) 75: Performance: 1298.744 0.018 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 (37 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: 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: 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: 0.002 0.001 192.7 75: (ns/day) (hour/ns) 75: Performance: 1166.448 0.021 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: 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: 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: 0.002 0.001 191.5 75: (ns/day) (hour/ns) 75: Performance: 1376.208 0.017 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: 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: 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: 0.002 0.001 190.7 75: (ns/day) (hour/ns) 75: Performance: 1644.579 0.015 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: 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: 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: 0.002 0.001 187.1 75: (ns/day) (hour/ns) 75: Performance: 1494.746 0.016 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: 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: 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: 0.002 0.001 190.4 75: (ns/day) (hour/ns) 75: Performance: 1592.296 0.015 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: 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: 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: 0.002 0.001 190.6 75: (ns/day) (hour/ns) 75: Performance: 1638.020 0.015 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 (34 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: 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: 0.003 0.001 193.7 75: (ns/day) (hour/ns) 75: Performance: 1025.911 0.023 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: 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: 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: 0.002 0.001 191.7 75: (ns/day) (hour/ns) 75: Performance: 1487.168 0.016 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: 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: 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: 0.002 0.001 164.3 75: (ns/day) (hour/ns) 75: Performance: 1284.394 0.019 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: 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: 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: 0.002 0.001 190.9 75: (ns/day) (hour/ns) 75: Performance: 1554.528 0.015 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: 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: 0.002 0.001 191.1 75: (ns/day) (hour/ns) 75: Performance: 1565.390 0.015 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: 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: 0.002 0.001 191.5 75: (ns/day) (hour/ns) 75: Performance: 1485.196 0.016 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 (32 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: 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: 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: 0.002 0.001 192.9 75: (ns/day) (hour/ns) 75: Performance: 1249.867 0.019 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: 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: 0.002 0.001 191.6 75: (ns/day) (hour/ns) 75: Performance: 1502.034 0.016 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: 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: 0.002 0.001 191.1 75: (ns/day) (hour/ns) 75: Performance: 1643.044 0.015 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: 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: 0.002 0.001 191.1 75: (ns/day) (hour/ns) 75: Performance: 1552.960 0.015 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: 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: 0.002 0.001 190.4 75: (ns/day) (hour/ns) 75: Performance: 1549.835 0.015 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: 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: 0.002 0.001 191.1 75: (ns/day) (hour/ns) 75: Performance: 1570.578 0.015 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 (30 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: 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: 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: 0.002 0.001 193.0 75: (ns/day) (hour/ns) 75: Performance: 1255.598 0.019 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: 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: 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1458.474 0.016 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: 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: 0.002 0.001 191.3 75: (ns/day) (hour/ns) 75: Performance: 1642.606 0.015 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: 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: 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: 0.002 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1533.630 0.016 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: 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: 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: 0.002 0.001 191.3 75: (ns/day) (hour/ns) 75: Performance: 1530.963 0.016 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: 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: 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: 0.002 0.001 191.1 75: (ns/day) (hour/ns) 75: Performance: 1462.629 0.016 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 (31 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: 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: 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: 0.002 0.001 192.8 75: (ns/day) (hour/ns) 75: Performance: 1342.324 0.018 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: 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: 0.002 0.001 192.2 75: (ns/day) (hour/ns) 75: Performance: 1509.395 0.016 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: 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: 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: 0.001 0.001 189.8 75: (ns/day) (hour/ns) 75: Performance: 2014.253 0.012 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: 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: 0.002 0.001 190.9 75: (ns/day) (hour/ns) 75: Performance: 1667.278 0.014 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: 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: 0.002 0.001 190.3 75: (ns/day) (hour/ns) 75: Performance: 1656.296 0.014 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: 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: 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: 0.002 0.001 189.7 75: (ns/day) (hour/ns) 75: Performance: 1632.162 0.015 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 (30 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: 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: 15 % of the run time was spent in domain decomposition, 75: 2 % 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: 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: 0.003 0.001 193.2 75: (ns/day) (hour/ns) 75: Performance: 1102.764 0.022 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: 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: 0.002 0.001 191.4 75: (ns/day) (hour/ns) 75: Performance: 1506.074 0.016 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: 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: 0.003 0.002 187.8 75: (ns/day) (hour/ns) 75: Performance: 942.059 0.025 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: 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: 0.003 0.002 185.4 75: (ns/day) (hour/ns) 75: Performance: 895.826 0.027 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: 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: 0.003 0.002 187.2 75: (ns/day) (hour/ns) 75: Performance: 937.614 0.026 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: 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: 0.003 0.002 187.9 75: (ns/day) (hour/ns) 75: Performance: 881.092 0.027 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 (49 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: 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: 21 % of the run time was 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 0.003 193.0 75: (ns/day) (hour/ns) 75: Performance: 549.415 0.044 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: 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: 0.003 0.001 189.4 75: (ns/day) (hour/ns) 75: Performance: 987.354 0.024 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: 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: 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 0.001 187.9 75: (ns/day) (hour/ns) 75: Performance: 1102.173 0.022 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: 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: 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 0.001 188.1 75: (ns/day) (hour/ns) 75: Performance: 1078.535 0.022 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: 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: 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: 0.002 0.001 188.0 75: (ns/day) (hour/ns) 75: Performance: 1174.229 0.020 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: 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: 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: 0.002 0.001 188.0 75: (ns/day) (hour/ns) 75: Performance: 1206.540 0.020 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 (56 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: 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: 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: 0.003 0.001 191.3 75: (ns/day) (hour/ns) 75: Performance: 1043.373 0.023 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: 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: 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: 0.002 0.001 189.1 75: (ns/day) (hour/ns) 75: Performance: 1246.453 0.019 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: 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: 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: 0.002 0.001 189.2 75: (ns/day) (hour/ns) 75: Performance: 1311.462 0.018 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: 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: 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: 0.002 0.001 185.2 75: (ns/day) (hour/ns) 75: Performance: 1254.320 0.019 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: 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: 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: 0.002 0.001 180.3 75: (ns/day) (hour/ns) 75: Performance: 1311.602 0.018 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: 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: 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: 0.002 0.001 189.5 75: (ns/day) (hour/ns) 75: Performance: 1356.212 0.018 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 (44 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: 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: 0.003 0.001 193.5 75: (ns/day) (hour/ns) 75: Performance: 1095.509 0.022 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: 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: 0.002 0.001 192.1 75: (ns/day) (hour/ns) 75: Performance: 1296.285 0.019 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: 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: 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: 0.002 0.001 191.6 75: (ns/day) (hour/ns) 75: Performance: 1661.433 0.014 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: 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: 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: 0.002 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1566.784 0.015 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: 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: 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: 0.002 0.001 191.3 75: (ns/day) (hour/ns) 75: Performance: 1573.185 0.015 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: 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: 0.002 0.001 192.7 75: (ns/day) (hour/ns) 75: Performance: 1288.558 0.019 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 (37 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: 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: 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: 0.002 0.001 191.0 75: (ns/day) (hour/ns) 75: Performance: 1190.338 0.020 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: 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: 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: 0.002 0.001 190.9 75: (ns/day) (hour/ns) 75: Performance: 1770.031 0.014 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: 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: 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1531.914 0.016 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: 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: 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: 0.002 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1506.995 0.016 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: 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: 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: 0.002 0.001 192.3 75: (ns/day) (hour/ns) 75: Performance: 1429.538 0.017 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: 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: 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: 0.002 0.001 191.8 75: (ns/day) (hour/ns) 75: Performance: 1436.371 0.017 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 (32 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: 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: 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: 0.002 0.001 193.0 75: (ns/day) (hour/ns) 75: Performance: 1252.408 0.019 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: 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: 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: 0.002 0.001 192.3 75: (ns/day) (hour/ns) 75: Performance: 1430.866 0.017 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: 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: 0.002 0.001 191.5 75: (ns/day) (hour/ns) 75: Performance: 1568.779 0.015 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: 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: 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: 0.002 0.001 191.5 75: (ns/day) (hour/ns) 75: Performance: 1539.379 0.016 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: 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: 0.002 0.001 191.9 75: (ns/day) (hour/ns) 75: Performance: 1509.764 0.016 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: 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: 0.002 0.001 191.8 75: (ns/day) (hour/ns) 75: Performance: 1485.196 0.016 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 (32 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: 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: 7.7%. 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: 4.6%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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: 0.003 0.002 192.7 75: (ns/day) (hour/ns) 75: Performance: 859.698 0.028 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: 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: 9.5%. 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: 5.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.7 % 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: 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: 0.003 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 927.242 0.026 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: 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: 11.9%. 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: 6.6%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.6 % 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: 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: 0.002 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1125.017 0.021 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: 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: 15.5%. 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: 8.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 8.2 % 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: 0.003 0.001 191.5 75: (ns/day) (hour/ns) 75: Performance: 986.879 0.024 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: 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: 12.0%. 75: The balanceable part of the MD step is 46%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 5.5%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.5 % 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: 0.003 0.002 192.4 75: (ns/day) (hour/ns) 75: Performance: 870.817 0.028 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: 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: 15.4%. 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: 8.1%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 8.1 % 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: 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: 0.003 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1024.120 0.023 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 (34 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 7.1%. 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: 4.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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: 0.003 0.002 192.9 75: (ns/day) (hour/ns) 75: Performance: 817.651 0.029 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 9.9%. 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: 5.6%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.6 % 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: 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: 0.003 0.002 191.5 75: (ns/day) (hour/ns) 75: Performance: 912.613 0.026 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 11.3%. 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: 6.5%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.5 % 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: 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: 0.003 0.001 191.5 75: (ns/day) (hour/ns) 75: Performance: 979.427 0.025 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 11.1%. 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: 6.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.2 % 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: 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: 0.003 0.002 191.7 75: (ns/day) (hour/ns) 75: Performance: 935.692 0.026 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 9.5%. 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: 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: 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: 0.003 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 900.672 0.027 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: 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 12.3%. 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: 6.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 6.9 % 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: 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: 0.003 0.002 192.1 75: (ns/day) (hour/ns) 75: Performance: 941.195 0.025 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 (35 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: 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: 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: 0.003 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 846.177 0.028 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: 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: 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: 0.003 0.001 188.4 75: (ns/day) (hour/ns) 75: Performance: 1104.841 0.022 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: 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: 0.003 0.001 189.5 75: (ns/day) (hour/ns) 75: Performance: 1067.231 0.022 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: 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: 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: 0.003 0.001 189.4 75: (ns/day) (hour/ns) 75: Performance: 1039.675 0.023 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: 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: 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: 0.003 0.001 189.8 75: (ns/day) (hour/ns) 75: Performance: 1009.851 0.024 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: 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: 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: 0.003 0.001 189.6 75: (ns/day) (hour/ns) 75: Performance: 1006.222 0.024 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 (34 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: 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: 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: 0.003 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 809.752 0.030 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: 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: 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: 0.003 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 822.399 0.029 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: 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: 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: 0.003 0.001 189.1 75: (ns/day) (hour/ns) 75: Performance: 1015.762 0.024 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: 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: 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: 0.003 0.002 189.1 75: (ns/day) (hour/ns) 75: Performance: 923.974 0.026 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: 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: 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: 0.003 0.002 189.4 75: (ns/day) (hour/ns) 75: Performance: 973.930 0.025 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: 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: 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: 0.003 0.002 189.5 75: (ns/day) (hour/ns) 75: Performance: 913.899 0.026 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 (35 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: 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: 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: 0.003 0.002 190.2 75: (ns/day) (hour/ns) 75: Performance: 858.201 0.028 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: 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: 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: 0.003 0.002 189.2 75: (ns/day) (hour/ns) 75: Performance: 915.257 0.026 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: 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: 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: 0.003 0.001 189.5 75: (ns/day) (hour/ns) 75: Performance: 999.528 0.024 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: 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: 0.003 0.002 180.7 75: (ns/day) (hour/ns) 75: Performance: 842.532 0.028 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: 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: 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: 0.003 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 908.441 0.026 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: 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: 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: 0.003 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 940.262 0.026 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 (35 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: 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: 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: 0.004 0.002 192.4 75: (ns/day) (hour/ns) 75: Performance: 718.102 0.033 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: 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: 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: 0.004 0.002 185.5 75: (ns/day) (hour/ns) 75: Performance: 716.390 0.034 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: 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: 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: 0.003 0.002 192.1 75: (ns/day) (hour/ns) 75: Performance: 851.028 0.028 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: 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: 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: 0.004 0.002 191.4 75: (ns/day) (hour/ns) 75: Performance: 774.430 0.031 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: 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: 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: 0.003 0.002 191.5 75: (ns/day) (hour/ns) 75: Performance: 805.886 0.030 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: 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: 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: 0.004 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 791.494 0.030 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 (36 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: 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: 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: 0.005 0.003 193.4 75: (ns/day) (hour/ns) 75: Performance: 539.079 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_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: 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: 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: 0.005 0.003 193.7 75: (ns/day) (hour/ns) 75: Performance: 528.353 0.045 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: 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: 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: 0.005 0.002 192.7 75: (ns/day) (hour/ns) 75: Performance: 603.241 0.040 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: 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: 18 % of the run time was 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 0.003 193.0 75: (ns/day) (hour/ns) 75: Performance: 550.889 0.044 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: 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: 18 % of the run time was 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 0.002 192.7 75: (ns/day) (hour/ns) 75: Performance: 591.143 0.041 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: 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: 18 % of the run time was 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: 576.997 0.042 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 (42 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: 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: 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: 0.004 0.002 192.5 75: (ns/day) (hour/ns) 75: Performance: 688.296 0.035 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: 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: 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: 0.004 0.002 191.3 75: (ns/day) (hour/ns) 75: Performance: 768.681 0.031 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: 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: 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: 0.004 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 795.018 0.030 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: 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: 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 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 767.436 0.031 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: 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: 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: 0.004 0.002 190.2 75: (ns/day) (hour/ns) 75: Performance: 760.098 0.032 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: 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: 13 % of the run time was 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: 742.106 0.032 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 (38 ms) 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (848 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 22 tests from 1 test suite ran. (862 ms total) 75: [ PASSED ] 22 tests. 75/81 Test #75: MdrunMpiCoordinationCouplingTestsTwoRanks ...... Passed 0.88 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: 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: 0.001 0.001 96.3 76: (ns/day) (hour/ns) 76: Performance: 1691.077 0.014 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: 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: 0.001 0.001 95.4 76: (ns/day) (hour/ns) 76: Performance: 2111.962 0.011 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: 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: 0.001 0.001 94.9 76: (ns/day) (hour/ns) 76: Performance: 2548.860 0.009 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: 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: 0.001 0.001 95.0 76: (ns/day) (hour/ns) 76: Performance: 2373.110 0.010 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: 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: 0.001 0.001 95.1 76: (ns/day) (hour/ns) 76: Performance: 2351.372 0.010 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: 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: 0.001 0.001 95.0 76: (ns/day) (hour/ns) 76: Performance: 2208.890 0.011 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 (1423 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: 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: 0.001 0.001 96.1 76: (ns/day) (hour/ns) 76: Performance: 1707.482 0.014 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: 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: 0.001 0.001 95.3 76: (ns/day) (hour/ns) 76: Performance: 2016.561 0.012 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: 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: 0.001 0.001 94.8 76: (ns/day) (hour/ns) 76: Performance: 2451.490 0.010 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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2358.573 0.010 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: 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: 0.001 0.001 95.1 76: (ns/day) (hour/ns) 76: Performance: 2155.561 0.011 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: 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: 0.001 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2280.857 0.011 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 (1384 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: 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: 0.001 0.001 96.2 76: (ns/day) (hour/ns) 76: Performance: 1786.715 0.013 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: 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: 0.001 0.001 95.0 76: (ns/day) (hour/ns) 76: Performance: 2188.488 0.011 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: 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: 0.001 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2604.902 0.009 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: 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: 0.001 0.001 94.5 76: (ns/day) (hour/ns) 76: Performance: 2383.208 0.010 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: 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: 0.001 0.001 94.9 76: (ns/day) (hour/ns) 76: Performance: 2379.526 0.010 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: 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: 0.001 0.001 94.7 76: (ns/day) (hour/ns) 76: Performance: 2322.124 0.010 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 (1385 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: 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: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 1653.851 0.015 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: 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: 0.001 0.001 95.2 76: (ns/day) (hour/ns) 76: Performance: 2094.728 0.011 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: 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: 0.001 0.001 94.1 76: (ns/day) (hour/ns) 76: Performance: 2483.109 0.010 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: 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: 0.001 0.001 94.7 76: (ns/day) (hour/ns) 76: Performance: 2244.296 0.011 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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2193.944 0.011 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: 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: 0.001 0.001 94.7 76: (ns/day) (hour/ns) 76: Performance: 2245.114 0.011 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 (1378 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: 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: 0.001 0.001 96.1 76: (ns/day) (hour/ns) 76: Performance: 1713.656 0.014 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: 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: 0.001 0.001 95.2 76: (ns/day) (hour/ns) 76: Performance: 2059.710 0.012 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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2366.728 0.010 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: 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: 0.001 0.001 94.7 76: (ns/day) (hour/ns) 76: Performance: 2305.611 0.010 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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2258.282 0.011 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: 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: 0.001 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2323.875 0.010 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 (1374 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1605.576 0.015 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: 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: 0.001 0.001 96.4 76: (ns/day) (hour/ns) 76: Performance: 2066.620 0.012 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: 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: 0.001 0.001 95.8 76: (ns/day) (hour/ns) 76: Performance: 2267.425 0.011 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: 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: 0.001 0.001 95.8 76: (ns/day) (hour/ns) 76: Performance: 2098.295 0.011 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: 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: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 2129.483 0.011 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: 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: 0.001 0.001 95.8 76: (ns/day) (hour/ns) 76: Performance: 2188.488 0.011 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 (1374 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: 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: 0.001 0.001 96.6 76: (ns/day) (hour/ns) 76: Performance: 1648.099 0.015 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: 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: 0.001 0.001 96.0 76: (ns/day) (hour/ns) 76: Performance: 2031.188 0.012 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: 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: 0.001 0.001 95.4 76: (ns/day) (hour/ns) 76: Performance: 2318.628 0.010 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: 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: 0.001 0.001 96.0 76: (ns/day) (hour/ns) 76: Performance: 2128.747 0.011 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: 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: 0.001 0.001 95.7 76: (ns/day) (hour/ns) 76: Performance: 2133.908 0.011 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: 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: 0.001 0.001 95.7 76: (ns/day) (hour/ns) 76: Performance: 2078.473 0.012 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 (1388 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: 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: 0.001 0.001 97.8 76: (ns/day) (hour/ns) 76: Performance: 1424.415 0.017 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: 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: 0.001 0.001 97.4 76: (ns/day) (hour/ns) 76: Performance: 1659.196 0.014 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: 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: 0.001 0.001 97.2 76: (ns/day) (hour/ns) 76: Performance: 1730.018 0.014 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: 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: 0.001 0.001 97.3 76: (ns/day) (hour/ns) 76: Performance: 1699.943 0.014 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: 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: 0.001 0.001 97.3 76: (ns/day) (hour/ns) 76: Performance: 1642.825 0.015 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: 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: 0.001 0.001 97.4 76: (ns/day) (hour/ns) 76: Performance: 1664.575 0.014 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 (1385 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: 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: 0.001 0.001 97.3 76: (ns/day) (hour/ns) 76: Performance: 1346.578 0.018 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1550.615 0.015 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: 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: 0.001 0.001 96.1 76: (ns/day) (hour/ns) 76: Performance: 1682.763 0.014 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: 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: 0.001 0.001 96.8 76: (ns/day) (hour/ns) 76: Performance: 1645.897 0.015 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: 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: 0.001 0.001 96.6 76: (ns/day) (hour/ns) 76: Performance: 1590.652 0.015 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: 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: 0.001 0.001 96.5 76: (ns/day) (hour/ns) 76: Performance: 1665.926 0.014 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 (1385 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1289.367 0.019 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: 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: 0.001 0.001 96.5 76: (ns/day) (hour/ns) 76: Performance: 1539.763 0.016 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: 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: 0.001 0.001 96.5 76: (ns/day) (hour/ns) 76: Performance: 1661.433 0.014 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: 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: 0.001 0.001 96.8 76: (ns/day) (hour/ns) 76: Performance: 1569.178 0.015 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: 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: 0.001 0.001 96.8 76: (ns/day) (hour/ns) 76: Performance: 1578.021 0.015 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1512.544 0.016 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 (1386 ms) 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (13867 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 10 tests from 1 test suite ran. (13882 ms total) 76: [ PASSED ] 10 tests. 76/81 Test #76: MdrunMpiCoordinationConstraintsTestsOneRank .... Passed 13.90 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: 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: 12.7%. 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: 6.9%. 77: 77: NOTE: 6.9 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.003 0.001 193.5 77: (ns/day) (hour/ns) 77: Performance: 1047.097 0.023 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: 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: 19.1%. 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: 9.5%. 77: 77: NOTE: 9.5 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 23 % 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: 0.003 0.001 193.6 77: (ns/day) (hour/ns) 77: Performance: 1123.069 0.021 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: 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: 21.5%. 77: The balanceable part of the MD step is 49%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 10.7%. 77: 77: NOTE: 10.7 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.002 0.001 192.6 77: (ns/day) (hour/ns) 77: Performance: 1252.153 0.019 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: 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: 21.3%. 77: The balanceable part of the MD step is 49%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 10.5%. 77: 77: NOTE: 10.5 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 10 % of the run time was spent in domain decomposition, 77: 5 % 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: 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: 0.002 0.001 192.1 77: (ns/day) (hour/ns) 77: Performance: 1283.056 0.019 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: 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: 19.7%. 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: 9.9%. 77: 77: NOTE: 9.9 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 11 % of the run time was spent in domain decomposition, 77: 5 % 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: 20 % 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: 0.002 0.001 192.1 77: (ns/day) (hour/ns) 77: Performance: 1233.105 0.019 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: 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: 24.5%. 77: The balanceable part of the MD step is 47%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 11.5%. 77: 77: NOTE: 11.5 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 10 % of the run time was spent in domain decomposition, 77: 5 % 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: 20 % 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: 0.002 0.001 192.2 77: (ns/day) (hour/ns) 77: Performance: 1207.841 0.020 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 (1601 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: 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: 15.2%. 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: 8.0%. 77: 77: NOTE: 8.0 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.003 0.002 190.1 77: (ns/day) (hour/ns) 77: Performance: 919.903 0.026 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: 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: 16.2%. 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: 8.7%. 77: 77: NOTE: 8.7 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 23 % 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: 0.002 0.001 192.4 77: (ns/day) (hour/ns) 77: Performance: 1161.828 0.021 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: 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: 17.6%. 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: 9.3%. 77: 77: NOTE: 9.3 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 23 % 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: 0.002 0.001 192.4 77: (ns/day) (hour/ns) 77: Performance: 1236.943 0.019 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: 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: 18.4%. 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: 9.9%. 77: 77: NOTE: 9.9 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 23 % 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: 0.002 0.001 192.3 77: (ns/day) (hour/ns) 77: Performance: 1189.419 0.020 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: 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: 17.1%. 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: 9.2%. 77: 77: NOTE: 9.2 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.002 0.001 192.1 77: (ns/day) (hour/ns) 77: Performance: 1154.318 0.021 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: 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: 18.7%. 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: 9.9%. 77: 77: NOTE: 9.9 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.002 0.001 191.9 77: (ns/day) (hour/ns) 77: Performance: 1207.368 0.020 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 (1575 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: 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: 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: 0.003 0.001 193.8 77: (ns/day) (hour/ns) 77: Performance: 995.008 0.024 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: 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: 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: 0.002 0.001 192.8 77: (ns/day) (hour/ns) 77: Performance: 1159.205 0.021 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: 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: 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: 0.002 0.001 191.7 77: (ns/day) (hour/ns) 77: Performance: 1333.606 0.018 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: 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: 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: 0.002 0.001 192.2 77: (ns/day) (hour/ns) 77: Performance: 1279.459 0.019 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: 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: 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: 0.002 0.001 189.4 77: (ns/day) (hour/ns) 77: Performance: 1185.299 0.020 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: 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: 8 % 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: 0.002 0.001 192.3 77: (ns/day) (hour/ns) 77: Performance: 1247.084 0.019 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 (1563 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: 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: 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: 0.003 0.001 193.5 77: (ns/day) (hour/ns) 77: Performance: 1018.448 0.024 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: 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: 8 % 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: 0.002 0.001 192.9 77: (ns/day) (hour/ns) 77: Performance: 1157.136 0.021 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: 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: 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: 0.002 0.001 192.3 77: (ns/day) (hour/ns) 77: Performance: 1319.326 0.018 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: 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: 8 % 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: 0.002 0.001 192.4 77: (ns/day) (hour/ns) 77: Performance: 1235.950 0.019 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: 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: 8 % 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: 0.002 0.001 191.8 77: (ns/day) (hour/ns) 77: Performance: 1251.390 0.019 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: 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: 8 % 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: 0.002 0.001 192.1 77: (ns/day) (hour/ns) 77: Performance: 1210.928 0.020 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 (1555 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: 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: 8 % 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: 0.003 0.001 193.4 77: (ns/day) (hour/ns) 77: Performance: 1042.402 0.023 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: 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: 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: 0.002 0.001 192.8 77: (ns/day) (hour/ns) 77: Performance: 1181.435 0.020 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: 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: 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: 0.002 0.001 189.5 77: (ns/day) (hour/ns) 77: Performance: 1180.869 0.020 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: 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: 8 % 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: 0.002 0.001 191.9 77: (ns/day) (hour/ns) 77: Performance: 1245.445 0.019 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: 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: 8 % 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: 0.002 0.001 191.9 77: (ns/day) (hour/ns) 77: Performance: 1184.046 0.020 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: 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: 8 % 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: 0.002 0.001 191.9 77: (ns/day) (hour/ns) 77: Performance: 1182.456 0.020 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 (1557 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: 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: 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: 0.003 0.001 194.6 77: (ns/day) (hour/ns) 77: Performance: 1017.187 0.024 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: 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: 8 % 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: 0.003 0.001 194.4 77: (ns/day) (hour/ns) 77: Performance: 1081.660 0.022 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: 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: 8 % 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: 0.002 0.001 193.8 77: (ns/day) (hour/ns) 77: Performance: 1167.442 0.021 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: 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: 0.002 0.001 191.3 77: (ns/day) (hour/ns) 77: Performance: 1588.806 0.015 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: 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: 0.002 0.001 193.6 77: (ns/day) (hour/ns) 77: Performance: 1203.123 0.020 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: 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: 0.002 0.001 193.2 77: (ns/day) (hour/ns) 77: Performance: 1195.187 0.020 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 (1557 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: 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: NOTE: 8 % 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: 0.003 0.002 194.6 77: (ns/day) (hour/ns) 77: Performance: 937.400 0.026 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: 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: NOTE: 8 % 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: 0.003 0.001 194.2 77: (ns/day) (hour/ns) 77: Performance: 1080.996 0.022 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: 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: NOTE: 8 % 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: 0.002 0.001 193.5 77: (ns/day) (hour/ns) 77: Performance: 1164.243 0.021 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: 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: 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: 0.003 0.001 193.4 77: (ns/day) (hour/ns) 77: Performance: 1108.419 0.022 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: 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: 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: 0.003 0.001 193.3 77: (ns/day) (hour/ns) 77: Performance: 1115.544 0.022 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: 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: NOTE: 8 % 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: 0.003 0.001 192.9 77: (ns/day) (hour/ns) 77: Performance: 1132.150 0.021 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 (1568 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: 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: 10.8%. 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: 6.4%. 77: 77: NOTE: 6.4 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 77: 77: NOTE: 12 % 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 0.002 193.5 77: (ns/day) (hour/ns) 77: Performance: 727.815 0.033 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: 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: 14.6%. 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: 8.7%. 77: 77: NOTE: 8.7 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.003 0.002 192.3 77: (ns/day) (hour/ns) 77: Performance: 853.386 0.028 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: 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: 19.2%. 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: 10.8%. 77: 77: NOTE: 10.8 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.003 0.002 191.8 77: (ns/day) (hour/ns) 77: Performance: 923.420 0.026 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: 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: 18.3%. 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: 10.2%. 77: 77: NOTE: 10.2 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.003 0.002 191.8 77: (ns/day) (hour/ns) 77: Performance: 890.967 0.027 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: 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: 21.0%. 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: 11.6%. 77: 77: NOTE: 11.6 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.003 0.002 192.0 77: (ns/day) (hour/ns) 77: Performance: 863.554 0.028 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: 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: 18.2%. 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: 9.3%. 77: 77: NOTE: 9.3 % of the available CPU time was lost due to load imbalance 77: in the domain decomposition. 77: You can consider manually changing the decomposition (option -dd); 77: e.g. by using fewer domains along the box dimension in which there is 77: considerable inhomogeneity in the simulated system. 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: 0.003 0.002 191.4 77: (ns/day) (hour/ns) 77: Performance: 833.019 0.029 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 (1610 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: 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: 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: 0.004 0.002 189.1 77: (ns/day) (hour/ns) 77: Performance: 671.967 0.036 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: 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: 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: 0.004 0.002 190.7 77: (ns/day) (hour/ns) 77: Performance: 780.118 0.031 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: 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: 8 % 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: 0.003 0.002 188.1 77: (ns/day) (hour/ns) 77: Performance: 821.412 0.029 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: 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: 8 % 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: 0.003 0.002 190.0 77: (ns/day) (hour/ns) 77: Performance: 818.086 0.029 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: 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: 0.004 0.002 190.3 77: (ns/day) (hour/ns) 77: Performance: 735.945 0.033 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: 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: 0.003 0.001 184.6 77: (ns/day) (hour/ns) 77: Performance: 1025.825 0.023 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 (1583 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: 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: 0.004 0.002 190.4 77: (ns/day) (hour/ns) 77: Performance: 636.853 0.038 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: 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: 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: 0.004 0.002 191.1 77: (ns/day) (hour/ns) 77: Performance: 791.138 0.030 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: 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: 8 % 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: 0.003 0.002 191.0 77: (ns/day) (hour/ns) 77: Performance: 802.736 0.030 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: 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: 8 % 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 0.002 190.8 77: (ns/day) (hour/ns) 77: Performance: 800.753 0.030 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: 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: 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 0.002 190.9 77: (ns/day) (hour/ns) 77: Performance: 743.674 0.032 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: 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: 8 % 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: 777.460 0.031 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 (1608 ms) 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (15780 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 10 tests from 1 test suite ran. (15795 ms total) 77: [ PASSED ] 10 tests. 77/81 Test #77: MdrunMpiCoordinationConstraintsTestsTwoRanks ... Passed 15.82 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: 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 2143155830 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: 0.93 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: 0.137 0.068 199.8 78: (ns/day) (hour/ns) 78: Performance: 26.559 0.904 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 (111 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: 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 2004705091 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: 0.93 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: 0.118 0.059 199.8 78: (ns/day) (hour/ns) 78: Performance: 30.774 0.780 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 (81 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: 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 -236064962 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: 0.93 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: 0.075 0.038 199.7 78: (ns/day) (hour/ns) 78: Performance: 48.014 0.500 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 (54 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: 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 -573530202 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: 0.93 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: 0.355 0.178 199.9 78: (ns/day) (hour/ns) 78: Performance: 49.121 0.489 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 (197 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: 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 -69715 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: 0.93 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: 0.098 0.049 199.8 78: (ns/day) (hour/ns) 78: Performance: 37.174 0.646 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 (65 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: 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 -340570258 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: 0.93 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: 0.098 0.049 199.8 78: (ns/day) (hour/ns) 78: Performance: 36.952 0.649 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 (66 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: 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 -608305203 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: 0.87 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: 0.026 0.013 199.2 78: (ns/day) (hour/ns) 78: Performance: 140.712 0.171 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 (28 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: 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: 0.027 0.014 199.1 78: (ns/day) (hour/ns) 78: Performance: 134.384 0.179 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 -1350594561 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: 0.87 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (28 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: 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 -419693062 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: 0.93 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: 0.126 0.063 199.8 78: (ns/day) (hour/ns) 78: Performance: 28.747 0.835 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 (81 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: 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 -553846020 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: 0.055 0.027 199.6 78: (ns/day) (hour/ns) 78: Performance: 66.114 0.363 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 (43 ms) 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest (762 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 10 tests from 1 test suite ran. (777 ms total) 78: [ PASSED ] 10 tests. 78/81 Test #78: MdrunFEPTests .................................. Passed 0.80 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: 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: 0.063 0.032 199.7 79: (ns/day) (hour/ns) 79: Performance: 57.207 0.420 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 (327 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: 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: NOTE: 12 % 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: 0.064 0.032 199.7 79: (ns/day) (hour/ns) 79: Performance: 56.773 0.423 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 (301 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: 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: NOTE: 12 % 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: 0.063 0.032 199.7 79: (ns/day) (hour/ns) 79: Performance: 57.406 0.418 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 (298 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: 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: 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: 0.063 0.032 199.6 79: (ns/day) (hour/ns) 79: Performance: 57.345 0.419 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 (305 ms) 79: [----------] 4 tests from PullTest/PullIntegrationTest (1232 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 4 tests from 1 test suite ran. (1247 ms total) 79: [ PASSED ] 4 tests. 79/81 Test #79: MdrunPullTests ................................. Passed 1.27 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: 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: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 197.7 80: (ns/day) (hour/ns) 80: Performance: 457.323 0.052 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: 0.003 0.002 191.6 80: (ns/day) (hour/ns) 80: Performance: 951.590 0.025 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 195.2 80: (ns/day) (hour/ns) 80: Performance: 948.075 0.025 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: 0.003 0.002 193.3 80: (ns/day) (hour/ns) 80: Performance: 881.849 0.027 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (13 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: 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: 0.003 0.001 194.2 80: (ns/day) (hour/ns) 80: Performance: 1086.716 0.022 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: 0.002 0.001 191.9 80: (ns/day) (hour/ns) 80: Performance: 1278.397 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (11 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: 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: 0.003 0.001 194.2 80: (ns/day) (hour/ns) 80: Performance: 1097.754 0.022 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: 0.003 0.002 194.1 80: (ns/day) (hour/ns) 80: Performance: 932.152 0.026 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (10 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: 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: 0.003 0.002 195.3 80: (ns/day) (hour/ns) 80: Performance: 860.298 0.028 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: 0.002 0.001 191.2 80: (ns/day) (hour/ns) 80: Performance: 1486.989 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (9 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: 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: 0.002 0.001 194.1 80: (ns/day) (hour/ns) 80: Performance: 1209.382 0.020 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: 0.003 0.001 194.2 80: (ns/day) (hour/ns) 80: Performance: 1100.106 0.022 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (9 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: 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: 0.002 0.001 194.7 80: (ns/day) (hour/ns) 80: Performance: 1215.107 0.020 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: 0.002 0.001 192.0 80: (ns/day) (hour/ns) 80: Performance: 1368.109 0.018 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (8 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: 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: 0.002 0.001 194.3 80: (ns/day) (hour/ns) 80: Performance: 1210.809 0.020 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: 0.002 0.001 192.6 80: (ns/day) (hour/ns) 80: Performance: 1442.424 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (8 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: 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: 0.004 0.002 195.3 80: (ns/day) (hour/ns) 80: Performance: 803.311 0.030 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: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 193.3 80: (ns/day) (hour/ns) 80: Performance: 1306.595 0.018 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (9 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: 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: 0.003 0.001 195.5 80: (ns/day) (hour/ns) 80: Performance: 991.565 0.024 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: 0.002 0.001 193.3 80: (ns/day) (hour/ns) 80: Performance: 1644.140 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.003 0.001 195.3 80: (ns/day) (hour/ns) 80: Performance: 1007.951 0.024 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: 0.002 0.001 191.7 80: (ns/day) (hour/ns) 80: Performance: 1549.835 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.003 0.002 193.5 80: (ns/day) (hour/ns) 80: Performance: 951.296 0.025 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: 0.002 0.001 192.7 80: (ns/day) (hour/ns) 80: Performance: 1440.738 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 193.6 80: (ns/day) (hour/ns) 80: Performance: 1457.094 0.016 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: 0.002 0.001 192.4 80: (ns/day) (hour/ns) 80: Performance: 1717.957 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 193.6 80: (ns/day) (hour/ns) 80: Performance: 1466.808 0.016 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: 0.002 0.001 192.0 80: (ns/day) (hour/ns) 80: Performance: 1628.494 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.003 0.001 195.0 80: (ns/day) (hour/ns) 80: Performance: 1124.401 0.021 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: 0.002 0.001 192.4 80: (ns/day) (hour/ns) 80: Performance: 1633.243 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 194.3 80: (ns/day) (hour/ns) 80: Performance: 1246.075 0.019 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: 0.002 0.001 193.8 80: (ns/day) (hour/ns) 80: Performance: 1509.949 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 194.2 80: (ns/day) (hour/ns) 80: Performance: 1280.522 0.019 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: 0.002 0.001 193.0 80: (ns/day) (hour/ns) 80: Performance: 1509.579 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 194.4 80: (ns/day) (hour/ns) 80: Performance: 1295.876 0.019 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: 0.002 0.001 193.4 80: (ns/day) (hour/ns) 80: Performance: 1504.418 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 195.6 80: (ns/day) (hour/ns) 80: Performance: 1244.564 0.019 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: 0.002 0.001 192.6 80: (ns/day) (hour/ns) 80: Performance: 1480.200 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (290 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: 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: 0.002 0.001 195.3 80: (ns/day) (hour/ns) 80: Performance: 1168.993 0.021 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: 0.002 0.001 192.3 80: (ns/day) (hour/ns) 80: Performance: 1366.895 0.018 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (279 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: 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: 0.002 0.001 194.2 80: (ns/day) (hour/ns) 80: Performance: 1208.908 0.020 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: 0.002 0.001 192.6 80: (ns/day) (hour/ns) 80: Performance: 1429.704 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (287 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: 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: 0.009 0.005 197.8 80: (ns/day) (hour/ns) 80: Performance: 325.940 0.074 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: 0.002 0.001 192.6 80: (ns/day) (hour/ns) 80: Performance: 1383.781 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (292 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: 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: 0.002 0.001 194.1 80: (ns/day) (hour/ns) 80: Performance: 1161.719 0.021 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: 0.002 0.001 192.5 80: (ns/day) (hour/ns) 80: Performance: 1333.173 0.018 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (289 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: 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: 0.002 0.001 194.1 80: (ns/day) (hour/ns) 80: Performance: 1219.195 0.020 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: 0.002 0.001 192.4 80: (ns/day) (hour/ns) 80: Performance: 1455.373 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (289 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: 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: 0.002 0.001 193.5 80: (ns/day) (hour/ns) 80: Performance: 1170.770 0.020 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: 0.002 0.001 192.1 80: (ns/day) (hour/ns) 80: Performance: 1404.604 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (290 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: 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: 0.003 0.001 194.4 80: (ns/day) (hour/ns) 80: Performance: 1135.384 0.021 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: 0.002 0.001 192.5 80: (ns/day) (hour/ns) 80: Performance: 1417.206 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (288 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: 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: 0.003 0.001 194.5 80: (ns/day) (hour/ns) 80: Performance: 1121.127 0.021 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: 0.002 0.001 193.4 80: (ns/day) (hour/ns) 80: Performance: 1301.626 0.018 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (286 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: 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: 0.003 0.001 194.4 80: (ns/day) (hour/ns) 80: Performance: 1065.847 0.023 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: 0.002 0.001 192.9 80: (ns/day) (hour/ns) 80: Performance: 1317.774 0.018 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (289 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: 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: 0.002 0.001 194.2 80: (ns/day) (hour/ns) 80: Performance: 1210.571 0.020 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: 0.002 0.001 192.9 80: (ns/day) (hour/ns) 80: Performance: 1461.935 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (283 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: 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: 0.002 0.001 194.4 80: (ns/day) (hour/ns) 80: Performance: 1166.337 0.021 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: 0.002 0.001 192.4 80: (ns/day) (hour/ns) 80: Performance: 1434.364 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (283 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: 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: 0.002 0.001 194.1 80: (ns/day) (hour/ns) 80: Performance: 1145.092 0.021 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: 0.002 0.001 192.4 80: (ns/day) (hour/ns) 80: Performance: 1403.644 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (288 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 (3908 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: 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: 0.001 0.001 191.3 80: (ns/day) (hour/ns) 80: Performance: 1936.685 0.012 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: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 195.1 80: (ns/day) (hour/ns) 80: Performance: 1474.885 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.002 0.001 191.7 80: (ns/day) (hour/ns) 80: Performance: 1680.009 0.014 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: 0.002 0.001 194.8 80: (ns/day) (hour/ns) 80: Performance: 1302.727 0.018 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 191.5 80: (ns/day) (hour/ns) 80: Performance: 1791.391 0.013 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: 0.002 0.001 194.4 80: (ns/day) (hour/ns) 80: Performance: 1426.394 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.001 0.001 191.8 80: (ns/day) (hour/ns) 80: Performance: 2031.858 0.012 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: 0.002 0.001 193.8 80: (ns/day) (hour/ns) 80: Performance: 1530.582 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.001 0.001 190.6 80: (ns/day) (hour/ns) 80: Performance: 1974.549 0.012 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: 0.002 0.001 193.8 80: (ns/day) (hour/ns) 80: Performance: 1267.873 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 191.4 80: (ns/day) (hour/ns) 80: Performance: 1702.292 0.014 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: 0.003 0.001 193.9 80: (ns/day) (hour/ns) 80: Performance: 1091.917 0.022 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.001 0.001 190.8 80: (ns/day) (hour/ns) 80: Performance: 1922.782 0.012 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: 0.002 0.001 193.6 80: (ns/day) (hour/ns) 80: Performance: 1443.438 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.001 0.001 191.2 80: (ns/day) (hour/ns) 80: Performance: 2046.709 0.012 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: 0.002 0.001 194.1 80: (ns/day) (hour/ns) 80: Performance: 1565.589 0.015 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.001 0.001 186.2 80: (ns/day) (hour/ns) 80: Performance: 1950.790 0.012 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: 0.002 0.001 193.2 80: (ns/day) (hour/ns) 80: Performance: 1297.787 0.018 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 191.4 80: (ns/day) (hour/ns) 80: Performance: 1661.433 0.014 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: 0.002 0.001 193.3 80: (ns/day) (hour/ns) 80: Performance: 1426.063 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.001 0.001 190.6 80: (ns/day) (hour/ns) 80: Performance: 1942.792 0.012 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: 0.002 0.001 192.9 80: (ns/day) (hour/ns) 80: Performance: 1412.656 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.001 0.001 190.8 80: (ns/day) (hour/ns) 80: Performance: 2004.749 0.012 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: 0.002 0.001 193.4 80: (ns/day) (hour/ns) 80: Performance: 1505.154 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.002 0.001 191.5 80: (ns/day) (hour/ns) 80: Performance: 1720.836 0.014 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: 0.002 0.001 192.9 80: (ns/day) (hour/ns) 80: Performance: 1435.367 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.001 0.001 190.7 80: (ns/day) (hour/ns) 80: Performance: 1953.264 0.012 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: 0.002 0.001 193.7 80: (ns/day) (hour/ns) 80: Performance: 1429.372 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.001 0.001 191.3 80: (ns/day) (hour/ns) 80: Performance: 1971.390 0.012 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: 0.002 0.001 193.6 80: (ns/day) (hour/ns) 80: Performance: 1471.362 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.006 0.003 197.1 80: (ns/day) (hour/ns) 80: Performance: 520.057 0.046 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: 0.002 0.001 195.3 80: (ns/day) (hour/ns) 80: Performance: 1281.055 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (283 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: 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: 0.005 0.003 196.4 80: (ns/day) (hour/ns) 80: Performance: 559.444 0.043 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: 0.002 0.001 195.2 80: (ns/day) (hour/ns) 80: Performance: 1270.487 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (283 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: 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: 0.004 0.002 195.2 80: (ns/day) (hour/ns) 80: Performance: 778.344 0.031 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: 0.002 0.001 195.2 80: (ns/day) (hour/ns) 80: Performance: 1292.884 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (283 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: 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: 0.004 0.002 195.1 80: (ns/day) (hour/ns) 80: Performance: 785.991 0.031 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: 0.002 0.001 194.5 80: (ns/day) (hour/ns) 80: Performance: 1268.917 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (282 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: 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: 0.004 0.002 195.2 80: (ns/day) (hour/ns) 80: Performance: 763.016 0.031 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: 0.002 0.001 191.1 80: (ns/day) (hour/ns) 80: Performance: 1229.905 0.020 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (279 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: 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: 0.004 0.002 195.8 80: (ns/day) (hour/ns) 80: Performance: 679.452 0.035 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: 0.002 0.001 194.3 80: (ns/day) (hour/ns) 80: Performance: 1224.770 0.020 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (280 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: 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: 0.005 0.003 196.4 80: (ns/day) (hour/ns) 80: Performance: 567.640 0.042 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: 0.002 0.001 193.9 80: (ns/day) (hour/ns) 80: Performance: 1235.083 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (282 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: 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: 0.004 0.002 195.8 80: (ns/day) (hour/ns) 80: Performance: 705.358 0.034 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: 0.002 0.001 193.6 80: (ns/day) (hour/ns) 80: Performance: 1287.750 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (283 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: 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: 0.004 0.002 195.0 80: (ns/day) (hour/ns) 80: Performance: 782.496 0.031 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: 0.002 0.001 194.1 80: (ns/day) (hour/ns) 80: Performance: 1255.470 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (279 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: 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: 0.004 0.002 195.3 80: (ns/day) (hour/ns) 80: Performance: 720.622 0.033 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: 0.002 0.001 193.6 80: (ns/day) (hour/ns) 80: Performance: 1256.495 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (274 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: 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: 0.004 0.002 195.6 80: (ns/day) (hour/ns) 80: Performance: 712.125 0.034 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: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 194.5 80: (ns/day) (hour/ns) 80: Performance: 1283.724 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (272 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: 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: 0.004 0.002 195.8 80: (ns/day) (hour/ns) 80: Performance: 718.688 0.033 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: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 194.0 80: (ns/day) (hour/ns) 80: Performance: 1292.613 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (273 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: 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: 0.004 0.002 195.3 80: (ns/day) (hour/ns) 80: Performance: 797.694 0.030 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: 0.002 0.001 194.2 80: (ns/day) (hour/ns) 80: Performance: 1280.256 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (271 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: 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: 0.005 0.002 196.0 80: (ns/day) (hour/ns) 80: Performance: 625.504 0.038 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: 0.002 0.001 193.7 80: (ns/day) (hour/ns) 80: Performance: 1270.750 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (276 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: 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: 0.005 0.003 196.3 80: (ns/day) (hour/ns) 80: Performance: 575.756 0.042 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: 0.002 0.001 194.0 80: (ns/day) (hour/ns) 80: Performance: 1295.603 0.019 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (274 ms) 80: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (4289 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: 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: 0.002 0.001 194.3 80: (ns/day) (hour/ns) 80: Performance: 1257.521 0.019 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: 0.002 0.001 191.4 80: (ns/day) (hour/ns) 80: Performance: 1488.426 0.016 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 ms) 80: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (7 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: 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: 0.002 0.001 191.2 80: (ns/day) (hour/ns) 80: Performance: 1716.999 0.014 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: 0.002 0.001 191.7 80: (ns/day) (hour/ns) 80: Performance: 1157.354 0.021 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (8 ms) 80: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (8 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 94 tests from 4 test suites ran. (8250 ms total) 80: [ PASSED ] 94 tests. 80/81 Test #80: MdrunSimulatorComparison ....................... Passed 8.28 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: 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: 3.8%. 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: 1.8%. 81: 81: 81: NOTE: 37 % 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: 0.007 0.003 193.9 81: (ns/day) (hour/ns) 81: Performance: 226.485 0.106 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 (17 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: 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: 3.6%. 81: The balanceable part of the MD step is 56%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.0%. 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: 0.006 0.003 192.7 81: (ns/day) (hour/ns) 81: Performance: 263.013 0.091 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 (15 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: 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: 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 0.002 185.5 81: (ns/day) (hour/ns) 81: Performance: 414.658 0.058 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 (17 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: 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: 0.003 0.001 188.3 81: (ns/day) (hour/ns) 81: Performance: 572.694 0.042 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 (14 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: 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: NOTE: 26 % 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: 0.002 0.001 188.4 81: (ns/day) (hour/ns) 81: Performance: 601.807 0.040 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 (11 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: 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: 25 % 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: 0.002 0.001 189.8 81: (ns/day) (hour/ns) 81: Performance: 640.513 0.037 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 (11 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: 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: 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: 0.002 0.001 187.1 81: (ns/day) (hour/ns) 81: Performance: 660.823 0.036 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 (9 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: 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: NOTE: 23 % 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: 0.002 0.001 190.3 81: (ns/day) (hour/ns) 81: Performance: 681.750 0.035 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 (9 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: 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: 9.6%. 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: 4.8%. 81: 81: 81: NOTE: 25 % 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: 0.002 0.001 191.5 81: (ns/day) (hour/ns) 81: Performance: 636.513 0.038 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 (7 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: 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: 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: 0.002 0.001 191.0 81: (ns/day) (hour/ns) 81: Performance: 717.758 0.033 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 (9 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: 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: NOTE: 25 % 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: 0.002 0.001 191.4 81: (ns/day) (hour/ns) 81: Performance: 703.059 0.034 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 (8 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: 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: 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: 0.003 0.001 193.3 81: (ns/day) (hour/ns) 81: Performance: 564.907 0.042 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 (8 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: 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: 23 % 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: 0.002 0.001 192.1 81: (ns/day) (hour/ns) 81: Performance: 653.605 0.037 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 (9 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: 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: 21 % 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: 0.002 0.001 192.8 81: (ns/day) (hour/ns) 81: Performance: 710.952 0.034 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 (8 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: 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: 23 % 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: 0.002 0.001 191.7 81: (ns/day) (hour/ns) 81: Performance: 764.800 0.031 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 (8 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: 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: 23 % 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: 0.002 0.001 191.6 81: (ns/day) (hour/ns) 81: Performance: 763.726 0.031 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 (8 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: 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: NOTE: 23 % 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: 0.002 0.001 191.8 81: (ns/day) (hour/ns) 81: Performance: 776.361 0.031 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 (8 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: 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: 22 % 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: 0.002 0.001 192.1 81: (ns/day) (hour/ns) 81: Performance: 790.090 0.030 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 (8 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: 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: 23 % 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: 0.002 0.001 191.8 81: (ns/day) (hour/ns) 81: Performance: 763.994 0.031 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 (8 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 (201 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 37 tests from 2 test suites ran. (215 ms total) 81: [ PASSED ] 37 tests. 81/81 Test #81: MdrunVirtualSiteTests .......................... Passed 0.24 sec 100% tests passed, 0 tests failed out of 81 Label Time Summary: GTest = 63.42 sec*proc (79 tests) IntegrationTest = 21.06 sec*proc (23 tests) MpiTest = 35.28 sec*proc (19 tests) QuickGpuTest = 4.15 sec*proc (15 tests) SlowTest = 39.93 sec*proc (13 tests) UnitTest = 2.43 sec*proc (43 tests) Total Test time (real) = 63.56 sec touch build-basic dh_testdir /usr/bin/make -j12 -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 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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 CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/errhandler.cpp make[3]: Entering 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 -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/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/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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-ffile-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 make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' 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' 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 -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' 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 -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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]: 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/build 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 -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -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 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 -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' 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 -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 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 -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/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/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/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 -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 make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 0%] Built target release-version-info cd /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 -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 cd /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 -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/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/atomic.cpp cd /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 -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 -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 && /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 -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/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 -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 -I/build/reproducible-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 make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/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 -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 [ 2%] Built target thread_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 -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]: 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/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 -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 && /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 -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/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 -Wno-missing-field-initializers 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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/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 -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 -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 -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 -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/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 -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/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 -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 make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 2%] Built target gmx_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 -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' [ 2%] Built target lmfit_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 -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 -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 CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/widemuldiv.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 -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/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 -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 -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 -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 mdrun_objlib 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' [ 4%] Built target scanner 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 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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/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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o 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/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 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/statepropagatordata.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 -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/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 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-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 -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' [ 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 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/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 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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 -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 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src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o 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 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/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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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/aarch64-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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/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/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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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 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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/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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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-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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-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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-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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-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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-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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-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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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 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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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 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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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 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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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 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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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 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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/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_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 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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 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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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/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_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 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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/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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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 -Wno-missing-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 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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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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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 -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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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 -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/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_setup.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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/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 -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 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-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/pbc.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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/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 -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 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi/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 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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/idef.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/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_density.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/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/src/gromacs && /usr/bin/mpicxx -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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_helix.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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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 -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/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 -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/src/gromacs && /usr/bin/mpicxx -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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_tcaf.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_wheel.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -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 -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 && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=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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CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/distance.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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 -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 -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 -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 -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 -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 -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 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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 -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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -DGMX_DOUBLE=0 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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/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 -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 -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/biaswriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs 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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_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 -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 -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/restcbt.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 -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 -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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 -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 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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 -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 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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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/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/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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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 && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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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 -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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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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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 /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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_context.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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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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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/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 -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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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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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 -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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=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 -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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/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 /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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 = 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()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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 = 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>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /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 -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 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>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 = 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>:: | ^~~~~~~~~~~~~~~~~~~ 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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 = 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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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/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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../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 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'/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: 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 -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 -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/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/interactions.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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-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 -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 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api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/particlesequencer.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 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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 -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 /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/gmx_objlib.dir/gmx.cpp.o 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 ../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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 -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 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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_objlib.dir/DependInfo.cmake --color= 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/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-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 -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 CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/errhandler.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/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.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 -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' cd /build/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 -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 make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -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 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 -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' 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 -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 cd /build/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 -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/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/atomic.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build 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 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 -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]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /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-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 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 [ 0%] Built target release-version-info 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/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 -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/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 -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 -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/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 -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-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 -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-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 -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-dp' 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 -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/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 -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 && /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 -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 CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/huffman.c [ 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 -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-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 -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 -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' 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 -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 [ 2%] Built target gmx_objlib 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 -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-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 -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 -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/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 -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-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 -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/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 -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-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 -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 CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/widemuldiv.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 -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 -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 -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 -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 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 -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 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' [ 4%] Built target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 4%] Built target scanner 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 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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 -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 -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 -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 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-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 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-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 -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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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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-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 -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 -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 -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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/aarch64-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 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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 -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 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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/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 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CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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/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 -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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/logger.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 -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 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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 -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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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CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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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 -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 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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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/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_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 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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_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 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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 -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 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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 -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 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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_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 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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 -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 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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_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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-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 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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 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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 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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 -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_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 -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_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 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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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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_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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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_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_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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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_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 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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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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_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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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_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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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_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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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_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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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_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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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_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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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_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_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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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_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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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_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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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_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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -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 -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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -Wno-missing-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 -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 -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 -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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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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-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 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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 -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -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 -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/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/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=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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src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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/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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlineparser.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/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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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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/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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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_setup.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/ga2la.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/gpuhaloexchange_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 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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 -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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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/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 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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 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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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -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 -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/group.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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 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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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security 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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 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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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/helpmanager.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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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 -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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 -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/idef.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/ifunc.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/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/residuetypes.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/symtab.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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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.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 -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/cluster_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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/cmat.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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_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 -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /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 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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 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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 -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 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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 -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 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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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /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 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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 -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 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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 -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 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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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_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 -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/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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 -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /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 -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 -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/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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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 -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -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 -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 -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-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 && /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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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 -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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 -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/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 -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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/readir.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/readrot.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/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/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/abstractdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 && 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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 -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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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 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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 -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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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/freevolume.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-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -MF CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/convert_tpr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/dump.cpp.o -MF CMakeFiles/libgromacs.dir/tools/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/dump.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/eneconv.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/make_ndx.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 -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 -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 -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/conformation_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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/network.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/nrnb.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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/gmxlib/nonbonded/nb_free_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/boxdeformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 && /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 -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 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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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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 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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 -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 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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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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 -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/rf_util.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/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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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-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 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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 -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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-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 -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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 -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -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 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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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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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 -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 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 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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 -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 -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 -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/manage_threading.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/pairs.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/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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 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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 -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 && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/fft/calcgrid.cpp.o -c /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 -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 -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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 && 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/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/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-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 -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/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/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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/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/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/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/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/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/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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -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 -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 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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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-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 -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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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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-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 -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -I/build/reproducible-path/gromacs-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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -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-dp/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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/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 -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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 /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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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/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 -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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 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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 -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 /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/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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 -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 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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>:: | ^~~~~~~~~~~~~~~~~~~ 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>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 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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 -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-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 -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 cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/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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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-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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-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 -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 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_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 -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 -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -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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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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/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 -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/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 -I/build/reproducible-path/gromacs-2022.5/src/gromacs/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 -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 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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/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 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CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_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 -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-dp/src/gromacs && /usr/bin/mpicxx 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/usr/lib/aarch64-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' /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/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 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 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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 -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 -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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/interactions.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 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CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/molecules.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 -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 -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 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o 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-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 -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 /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/gmx_objlib.dir/gmx.cpp.o 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 -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 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 -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 -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 -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 -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/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 -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-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 -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/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 -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-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 -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-dp/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 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_mpi_d.so.7.0.0 /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lm cd /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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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/CMakeFiles/testutils.dir/filematchers.cpp.o -MF CMakeFiles/testutils.dir/filematchers.cpp.o.d -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/filematchers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils && /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/testutils -I/build/reproducible-path/gromacs-2022.5/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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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/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/applied_forces/awh/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= 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/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build 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/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake --color= 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]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make 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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/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 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src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build 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 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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/mpi' /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 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\" -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 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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 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/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -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/mpi/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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'/build/reproducible-path/gromacs-2022.5/build/mpi' 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 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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/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 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/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 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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/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 -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target utility-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/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/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2022.5/build/mpi/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/mpi' /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/mpi' 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 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src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-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/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 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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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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'/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target testutils-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/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/applied_forces/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-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/src/gromacs/mdlib/tests/constrtestrunners.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 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-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 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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 -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 -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/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 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'/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target nblib_test_infrastructure /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 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/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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/energydrifttracker.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 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CMakeFiles/density_fitting_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/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 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/build/reproducible-path/gromacs-2022.5/src/testutils/tests/testasserts_tests.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 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/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.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 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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/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 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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/expanded.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 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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target applied_forces-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 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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 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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/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o 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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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 66%] Built target nbnxm-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/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 -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/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 -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 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--color= 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 -I/build/reproducible-path/gromacs-2022.5/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 -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/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 -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/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 -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 cd /build/reproducible-path/gromacs-2022.5/build/mpi/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/mpi/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" 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 -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 /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 66%] 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/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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -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/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 -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/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 -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/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 -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/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 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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/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 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 -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/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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 67%] Built target domdec-test /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/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/hardware/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -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/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 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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 -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 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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 -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/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 -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/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 -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/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 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-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_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 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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 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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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 67%] Built target domdec-mpi-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/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/math/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests 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'/build/reproducible-path/gromacs-2022.5/build/mpi' [ 68%] Built target fft-test 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/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= [ 70%] Built target qmmm_applied_forces-test /usr/bin/make -f 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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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-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/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\" 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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 -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/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 -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/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 -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/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 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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/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 -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/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' [ 70%] Built target mdrunutility-test-shared /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 && 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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/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 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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 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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 -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/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" "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_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 70%] Built target listed_forces-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/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 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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/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 -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 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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 -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/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-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/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_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 72%] Built target mdspan-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 -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/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 -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/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 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-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 -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_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/settletestrunners_gpu.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 -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/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 -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/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\" 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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 -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/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 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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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests/helpwritercontext.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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-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/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 -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_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/device_buffer.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 -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/gammadistribution.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 72%] Built target ewald-test /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/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/restraint/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= make[4]: 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 -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 -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 /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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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/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 -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 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 74%] Built target onlinehelp-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 -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/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 -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/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 -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/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-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/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_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 74%] Built target gpu_utils-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 -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/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-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 -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 -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/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-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/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_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 mdlib-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 -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/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 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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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 restraintpotential-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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 timing-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 -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/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 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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/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 -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/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 -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/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 -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/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 -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/mpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 75%] Built target taskassignment-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= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target pbcutil-test 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 -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/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 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-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 78%] Built target mdtypes-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]: 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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests/entropy.cpp [ 78%] 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 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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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 78%] Built target compat-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/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/pdb2gmx1-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/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/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=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/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 -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/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 -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/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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/neldermead.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 -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 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 -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/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 -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 -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/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 -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 -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/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 -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/mpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 78%] 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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -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/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 -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 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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 -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 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 -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/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 -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 78%] Built target gmxana-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 -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/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 -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/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 -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/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/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 -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/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 -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/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 -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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 78%] Built target pdb2gmx1-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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 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 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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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/mpi' [ 78%] Built target pdb2gmx2-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 -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/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 -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/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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 79%] Built target topology-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend 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 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.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/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= 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 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 /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/keyvaluetreetransform.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 -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/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 -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/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 -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_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_vector_operations.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 -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/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 -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 /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_math.cpp:169:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 169 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 79%] Built target energyanalysis-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 81%] 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 -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 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/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 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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/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 -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/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 -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/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\" 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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 -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/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 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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/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 -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/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 -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 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o 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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-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/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_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 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 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 /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' [ 81%] Built target analysisdata-test-shared /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 -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' [ 82%] Built target simd-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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 83%] Built target gmxpreprocess-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 -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/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 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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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-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-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/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 -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 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 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-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 -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/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 -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/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 -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/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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/fileioxdrserializer.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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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/mpi' [ 83%] Built target tool-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 -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/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 -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/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/xvgio.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 -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/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-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 -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/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 -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/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 85%] Built target mdrun-output-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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 /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/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= 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 85%] Built target options-test /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 -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 /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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' [ 85%] Built target fileio-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 -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/mpi' [ 85%] 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/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= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /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/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 -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/mpi' [ 86%] Built target math-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/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= 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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/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 -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 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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/orires.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 86%] Built target coordinateio-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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 /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/mpi' [ 86%] 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 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/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 -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 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 -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 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 -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/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 -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 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 -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/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 -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/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 -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\" -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 -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 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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-single-rank-algorithms-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 -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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-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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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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\" 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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 -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/__/__/__/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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/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 -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/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 -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/__/__/__/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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 86%] 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/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-basic-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-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/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 -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/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 -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/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 -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/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-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/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_mpi.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/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 -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/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 -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/mpi' [ 86%] Built target mdrun-mpi-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/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-coupling-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-coupling-test.dir/build.make 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--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 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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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 86%] Built target selection-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-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 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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -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/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 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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/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 -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/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-constraints-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 -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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/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 -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/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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 87%] Built target mdrun-fep-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/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-integrator-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-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/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 /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/integrator.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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 89%] Built target mdrun-mpi-coordination-constraints-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/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-setup-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-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/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\" -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 -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 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 -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/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 -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 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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 90%] 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/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-tpr-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-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/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 -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 -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/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-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 -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/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\" 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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 -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 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 -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/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 -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/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-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-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_mpi.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 91%] Built target mdrun-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 /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 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/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 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 -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 /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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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' [ 91%] Built target mdrun-vsites-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/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 /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake --color= 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 -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 CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/typetraits.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /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/mpi' 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] Built target mdrun-simulator-comparison-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/util/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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/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 -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_mpi.so.7.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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-non-integrator-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 91%] Built target mdrun-mpi-coordination-basic-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/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/commandline/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /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/mpi' 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] Built target mdrun-mpi-coordination-coupling-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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] 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/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 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/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\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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 -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/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 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-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/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 -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/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 -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/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 -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/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 -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/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 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/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\" -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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] 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/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= 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 -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/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 -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/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 -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/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 -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-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/cmake -E cmake_link_script CMakeFiles/nblib-integrator-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-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] Built target mdrun-pull-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/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 -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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] Built target nblib-integrator-test 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 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp /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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a 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 -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' [ 91%] 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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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' [ 91%] Built target mdrunutility-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 -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 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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 93%] Built target utility-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 -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/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 -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/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 -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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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 -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 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 94%] Built target mdrunutility-mpi-test cd 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-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 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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/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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-I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/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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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 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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 -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 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:118:9: warning: iteration 2147483647 invokes undefined behavior [-Waggressive-loop-optimizations] 118 | for (int i = 0; i < count; ++i) | ^~~ /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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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/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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 98%] Built target trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 98%] Built target nblib-listed-forces-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/aarch64-linux-gnu/12/libgomp.so /usr/lib/aarch64-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 /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 (12 ms) 1: [----------] 8 tests from NBlibTest (13 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 (7 ms) 1: [----------] 1 test from LinearChainDataFixture (7 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. (22 ms total) 1: [ PASSED ] 44 tests. 1/81 Test #1: NbLibListedForcesTests ......................... Passed 0.16 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 0.01 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 5.324894 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 0.12 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 (1 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. (1 ms total) 5: [ PASSED ] 56 tests. 5/81 Test #5: NbLibSetupTests ................................ Passed 0.14 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 (17 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 (7 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 (7 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 (9 ms) 6: [----------] 4 tests from TprReaderTest (42 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 4 tests from 1 test suite ran. (46 ms total) 6: [ PASSED ] 4 tests. 6/81 Test #6: NbLibTprTests .................................. Passed 0.18 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 (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 (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 (3 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 20 tests from 1 test suite ran. (3 ms total) 7: [ PASSED ] 20 tests. 7/81 Test #7: NbLibIntegrationTests .......................... Passed 0.13 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 0.13 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 (1 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 (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 (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 (2 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 (0 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 59 tests from 5 test suites ran. (4 ms total) 9: [ PASSED ] 59 tests. 9/81 Test #9: TestUtilsUnitTests ............................. Passed 0.13 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 (0 ms) 10: [----------] 1 test from MpiSelfTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/81 Test #10: TestUtilsMpiUnitTests .......................... Passed 0.14 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 (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 (0 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 (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 (0 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 (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. (4 ms total) 11: [ PASSED ] 386 tests. 11: 11: YOU HAVE 1 DISABLED TEST 11: 11/81 Test #11: UtilityUnitTests ............................... Passed 0.15 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 (0 ms) 12: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 12: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 12: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 2 tests from 1 test suite ran. (0 ms total) 12: [ PASSED ] 2 tests. 12/81 Test #12: UtilityMpiUnitTests ............................ Passed 0.17 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 (2 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 (7 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 72 tests from 1 test suite ran. (7 ms total) 13: [ PASSED ] 72 tests. 13/81 Test #13: GmxlibTests .................................... Passed 0.14 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 (0 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 (5 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (4 ms) 14: [----------] 14 tests from WithParameters/ConstraintsTest (13 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 (0 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 (4 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 (18 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 (3 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 (0 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 (15 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 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 14: [----------] 13 tests from WithParameters/SettleTest (4 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 155 tests from 17 test suites ran. (56 ms total) 14: [ PASSED ] 155 tests. 14/81 Test #14: MdlibUnitTest .................................. Passed 0.21 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 (0 ms) 15: [----------] 1 test from biasGridTest (0 ms total) 15: 15: [----------] 1 test from BiasFepLambdaStateTest 15: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 15: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 15: [----------] 1 test from BiasFepLambdaStateTest (1 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 (1 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 (3 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (3 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (2 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (3 ms) 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (13 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 20 tests from 7 test suites ran. (18 ms total) 15: [ PASSED ] 20 tests. 15/81 Test #15: AwhTest ........................................ Passed 0.15 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 0.13 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 1978645719 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 (2 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 -109053731 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 (2 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 -1348897793 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 (2 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 -184720129 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 (6 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 1069444971 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 (6 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 -1097485097 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 (2 ms) 17: [----------] 7 tests from QMMMTopologyPreprocessorTest (23 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 (0 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. (24 ms total) 17: [ PASSED ] 21 tests. 17/81 Test #17: QMMMAppliedForcesUnitTest ...................... Passed 0.15 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 0.14 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 (2 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 (2 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 (1 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 (0 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 (1 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 (1 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 (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 132 tests from 9 test suites ran. (10 ms total) 19: [ PASSED ] 132 tests. 19/81 Test #19: ListedForcesTest ............................... Passed 0.16 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 0.13 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 (0 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 (1 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 (1 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 (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 60 tests from 7 test suites ran. (4 ms total) 21: [ PASSED ] 60 tests. 21/81 Test #21: CommandLineUnitTests ........................... Passed 0.13 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 0.12 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. (1 ms total) 23: [ PASSED ] 4 tests. 23/81 Test #23: DomDecMpiTests ................................. Passed 0.21 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (1 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 (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 (0 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 (1 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 (1 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 (1 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 (1 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 (1 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 (0 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 (1 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 (1 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 (1 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (0 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 (1 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 (0 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 (1 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 (1 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 (0 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 (1 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 (1 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 (1 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 (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 (0 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 (0 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 (0 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 (1 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 (1 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 (1 ms) 24: [----------] 108 tests from Pme_SplineAndSpreadTest (71 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_ (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_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_ (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_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 (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 (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 (7 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 (2 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 (3 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_ (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_ (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 (6 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 (7 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 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 24: 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (0 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 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (0 ms) 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (18 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 407 tests from 9 test suites ran. (119 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 0.25 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 (2 ms) 25: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (3 ms) 25: [----------] 2 tests from ManyFFTTest (6 ms total) 25: 25: [----------] 1 test from FFTTest 25: [ RUN ] FFTTest.Real2DLength18_15Test 25: [ OK ] FFTTest.Real2DLength18_15Test (1 ms) 25: [----------] 1 test from FFTTest (1 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 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 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 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (2 ms) 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (7 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 (0 ms) 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 25: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 15 tests from 4 test suites ran. (16 ms total) 25: [ PASSED ] 15 tests. 25/81 Test #25: FFTUnitTests ................................... Passed 0.14 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. (0 ms total) 26: [ PASSED ] 64 tests. 26/81 Test #26: GpuUtilsUnitTests .............................. Passed 0.15 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 (0 ms) 27: [----------] 1 test from CpuInfoTest (0 ms total) 27: 27: [----------] 4 tests from HardwareTopologyTest 27: [ RUN ] HardwareTopologyTest.Execute 27: [ OK ] HardwareTopologyTest.Execute (5 ms) 27: [ RUN ] HardwareTopologyTest.HwlocExecute 27: [ OK ] HardwareTopologyTest.HwlocExecute (4 ms) 27: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 27: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (3 ms) 27: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 27: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (3 ms) 27: [----------] 4 tests from HardwareTopologyTest (17 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 (0 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 (2 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 (2 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 (0 ms) 27: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (0 ms total) 27: 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 27: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 27: 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 27: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (1 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 21 tests from 9 test suites ran. (27 ms total) 27: [ PASSED ] 21 tests. 27/81 Test #27: HardwareUnitTests .............................. Passed 0.19 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 (15 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (12 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 28: [----------] 12 tests from DensitySimilarityTest (30 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 (0 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 (12 ms) 28: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 28: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 28: [----------] 2 tests from NelderMead (12 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 (2 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 (2 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. (47 ms total) 28: [ PASSED ] 301 tests. 28/81 Test #28: MathUnitTests .................................. Passed 0.19 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 (0 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 (2 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 17 tests from 1 test suite ran. (2 ms total) 29: [ PASSED ] 17 tests. 29/81 Test #29: MdrunUtilityUnitTests .......................... Passed 0.13 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 (41 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 (42 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 (7 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 13 tests from 2 test suites ran. (49 ms total) 30: [ PASSED ] 13 tests. 30/81 Test #30: MdrunUtilityMpiUnitTests ....................... Passed 0.21 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 0.13 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 (3 ms) 32: [----------] 2 tests from CheckpointDataTest (4 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 (1 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. (5 ms total) 32: [ PASSED ] 93 tests. 32/81 Test #32: MdtypesUnitTest ................................ Passed 0.14 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. (1 ms total) 33: [ PASSED ] 22 tests. 33/81 Test #33: OnlineHelpUnitTests ............................ Passed 0.15 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 (1 ms) 34: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 34: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 34: [----------] 5 tests from AbstractOptionStorageTest (1 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. (3 ms total) 34: [ PASSED ] 111 tests. 34/81 Test #34: OptionsUnitTests ............................... Passed 0.14 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 (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 (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 (4 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 33 tests from 5 test suites ran. (4 ms total) 35: [ PASSED ] 33 tests. 35/81 Test #35: PbcutilUnitTest ................................ Passed 0.13 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 (0 ms) 36: [----------] 1 test from TabulatedNormalDistributionTableTest (0 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. (1 ms total) 36: [ PASSED ] 44 tests. 36/81 Test #36: RandomUnitTests ................................ Passed 0.13 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 0.13 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 (0 ms) 38: [ RUN ] SplineTableTest/0.Sinc 38: [ OK ] SplineTableTest/0.Sinc (0 ms) 38: [ RUN ] SplineTableTest/0.LJ12 38: [ OK ] SplineTableTest/0.LJ12 (5 ms) 38: [ RUN ] SplineTableTest/0.PmeCorrection 38: [ OK ] SplineTableTest/0.PmeCorrection (0 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 (9 ms) 38: [ RUN ] SplineTableTest/0.ThreeFunctions 38: [ OK ] SplineTableTest/0.ThreeFunctions (10 ms) 38: [ RUN ] SplineTableTest/0.Simd 38: [ OK ] SplineTableTest/0.Simd (2 ms) 38: [ RUN ] SplineTableTest/0.SimdTwoFunctions 38: [ OK ] SplineTableTest/0.SimdTwoFunctions (8 ms) 38: [----------] 10 tests from SplineTableTest/0 (37 ms total) 38: 38: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 38: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 38: [ RUN ] SplineTableTest/1.Sinc 38: [ OK ] SplineTableTest/1.Sinc (0 ms) 38: [ RUN ] SplineTableTest/1.LJ12 38: [ OK ] SplineTableTest/1.LJ12 (0 ms) 38: [ RUN ] SplineTableTest/1.PmeCorrection 38: [ OK ] SplineTableTest/1.PmeCorrection (0 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 (1 ms) 38: [ RUN ] SplineTableTest/1.ThreeFunctions 38: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 38: [ RUN ] SplineTableTest/1.Simd 38: [ OK ] SplineTableTest/1.Simd (0 ms) 38: [ RUN ] SplineTableTest/1.SimdTwoFunctions 38: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 38: [----------] 10 tests from SplineTableTest/1 (6 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 20 tests from 2 test suites ran. (44 ms total) 38: [ PASSED ] 20 tests. 38/81 Test #38: TableUnitTests ................................. Passed 0.17 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 0.12 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 0.14 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 (0 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. (1 ms total) 41: [ PASSED ] 40 tests. 41/81 Test #41: TopologyTest ................................... Passed 0.17 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 0.12 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 (0 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 (0 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 (0 ms) 43: [ RUN ] SimdMathTest.exp2Unsafe 43: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 43: [ RUN ] SimdMathTest.exp 43: [ OK ] SimdMathTest.exp (0 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 (0 ms) 43: [ RUN ] SimdMathTest.erfc 43: [ OK ] SimdMathTest.erfc (0 ms) 43: [ RUN ] SimdMathTest.sin 43: [ OK ] SimdMathTest.sin (0 ms) 43: [ RUN ] SimdMathTest.cos 43: [ OK ] SimdMathTest.cos (0 ms) 43: [ RUN ] SimdMathTest.tan 43: [ OK ] SimdMathTest.tan (0 ms) 43: [ RUN ] SimdMathTest.asin 43: [ OK ] SimdMathTest.asin (0 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 (0 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 (0 ms) 43: [ RUN ] SimdMathTest.cbrtSingleAccuracy 43: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 43: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 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 (0 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 43: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracy 43: [ OK ] SimdMathTest.expSingleAccuracy (1 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 (0 ms) 43: [ RUN ] SimdMathTest.erfcSingleAccuracy 43: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.sinSingleAccuracy 43: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.cosSingleAccuracy 43: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.tanSingleAccuracy 43: [ OK ] SimdMathTest.tanSingleAccuracy (0 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 (17 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. (18 ms total) 43: [ PASSED ] 288 tests. 43/81 Test #43: SimdUnitTests .................................. Passed 0.16 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 0.17 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 (387 ms) 45: [----------] 1 test from GmxChiTest (433 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 (11 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 (1 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 (15 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 (6 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 (0 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 (0 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 (0 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 (0 ms) 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (11 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 22 tests from 4 test suites ran. (461 ms total) 45: [ PASSED ] 22 tests. 45/81 Test #45: GmxAnaTest ..................................... Passed 0.62 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 (1 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 452975935 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 (159 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 -234946561 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 (143 ms) 46: [----------] 2 tests from GenionTest (302 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 (0 ms) 46: [----------] 1 test from GenRestrTest (0 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 -34369799 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 -364939529 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 (2 ms) 46: [----------] 1 test from GromppDirectiveTest (2 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 (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/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 (0 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 (0 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 (3 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 (0 ms) 46: [----------] 5 tests from InsertMoleculesTest (6 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (0 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (0 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 (0 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 (1 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 (0 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 (0 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 (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (0 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (0 ms) 46: [----------] 34 tests from GetIrTest (35 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 (3 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 (22 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 (21 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 (10 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 (89 ms) 46: [----------] 5 tests from SolvateTest (146 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 (2 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 (1 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 (2 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 (1 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 (0 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 (1 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 (1 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 (2 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 (1 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 (1 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 (1 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 (1 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 (0 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 (0 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 (1 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 (1 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 (0 ms) 46: [----------] 18 tests from SinglePeptideFragments/EditconfTest (28 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 90 tests from 11 test suites ran. (525 ms total) 46: [ PASSED ] 90 tests. 46/81 Test #46: GmxPreprocessTests ............................. Passed 0.68 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 (24 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 (23 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 (21 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 (20 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 (89 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 (23 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 (26 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 (25 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 (23 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 (99 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 (20 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 (24 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 (29 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 (24 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 (92 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 (25 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 (25 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 (24 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 (22 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 (99 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 (22 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 (25 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 (26 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 (22 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 (88 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 (23 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 (25 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 (24 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 (22 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 (99 ms) 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1151 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 30 tests from 1 test suite ran. (1151 ms total) 47: [ PASSED ] 30 tests. 47/81 Test #47: Pdb2gmx1Test ................................... Passed 1.28 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 (33 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 (29 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 (23 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 (23 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 (59 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 (28 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 (29 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 (21 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 (20 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 (55 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 (20 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 (22 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 (20 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 (19 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 (54 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 (21 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 (23 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 (21 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 (20 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 (56 ms) 48: [----------] 20 tests from G43a1/Pdb2gmxTest (607 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 (22 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 (24 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 (25 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 (22 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 (56 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 (23 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 (27 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 (24 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 (23 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 (59 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 (22 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 (26 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 (23 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 (23 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 (58 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 (23 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 (26 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 (24 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 (23 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 (62 ms) 48: [----------] 20 tests from G53a6/Pdb2gmxTest (625 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 40 tests from 2 test suites ran. (1233 ms total) 48: [ PASSED ] 40 tests. 48/81 Test #48: Pdb2gmx2Test ................................... Passed 1.38 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 (28 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 (26 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 (25 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 (23 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 (92 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 (25 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 (28 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 (26 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 (24 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 (103 ms) 49: [----------] 10 tests from Amber/Pdb2gmxTest (406 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 (10 ms) 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest (10 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 (24 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 (25 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 (25 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 (24 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 (90 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 (10 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 (24 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 (26 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 (24 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 (22 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 (96 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 (11 ms) 49: [----------] 12 tests from Charmm/Pdb2gmxTest (407 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 (23 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 (21 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 (23 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 (19 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 (23 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 (20 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 (23 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 (21 ms) 49: [----------] 8 tests from ChainSep/Pdb2gmxTest (176 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 (12 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 (13 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 (13 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 (12 ms) 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest (53 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 (658 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 (76 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 (1318 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 (77 ms) 49: [----------] 4 tests from Cyclic/Pdb2gmxTest (2131 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 39 tests from 6 test suites ran. (3184 ms total) 49: [ PASSED ] 39 tests. 49/81 Test #49: Pdb2gmx3Test ................................... Passed 3.32 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 (11 ms) 50: [ RUN ] AutocorrTest.EacNoNormalize 50: [ OK ] AutocorrTest.EacNoNormalize (7 ms) 50: [ RUN ] AutocorrTest.EacCos 50: [ OK ] AutocorrTest.EacCos (19 ms) 50: [ RUN ] AutocorrTest.EacVector 50: [ OK ] AutocorrTest.EacVector (30 ms) 50: [ RUN ] AutocorrTest.EacRcross 50: [ OK ] AutocorrTest.EacRcross (0 ms) 50: [ RUN ] AutocorrTest.EacP0 50: [ OK ] AutocorrTest.EacP0 (29 ms) 50: [ RUN ] AutocorrTest.EacP1 50: [ OK ] AutocorrTest.EacP1 (27 ms) 50: [ RUN ] AutocorrTest.EacP2 50: [ OK ] AutocorrTest.EacP2 (35 ms) 50: [ RUN ] AutocorrTest.EacP3 50: [ OK ] AutocorrTest.EacP3 (2 ms) 50: [ RUN ] AutocorrTest.EacP4 50: [ OK ] AutocorrTest.EacP4 (17 ms) 50: [----------] 10 tests from AutocorrTest (182 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 (0 ms) 50: [ RUN ] ExpfitTest.EffnEXP5 50: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 50: [ RUN ] ExpfitTest.EffnEXP7 50: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 50: [ RUN ] ExpfitTest.EffnEXP9 50: [ OK ] ExpfitTest.EffnEXP9 (8 ms) 50: [ RUN ] ExpfitTest.EffnERF 50: [ OK ] ExpfitTest.EffnERF (1 ms) 50: [ RUN ] ExpfitTest.EffnERREST 50: [ OK ] ExpfitTest.EffnERREST (1 ms) 50: [ RUN ] ExpfitTest.EffnVAC 50: [ OK ] ExpfitTest.EffnVAC (2 ms) 50: [ RUN ] ExpfitTest.EffnPRES 50: [ OK ] ExpfitTest.EffnPRES (6 ms) 50: [----------] 10 tests from ExpfitTest (25 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. (210 ms total) 50: [ PASSED ] 21 tests. 50/81 Test #50: CorrelationsTest ............................... Passed 0.35 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 (1 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 (1 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 (1 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 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 (3 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 (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 (2 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 (0 ms total) 51: 51: [----------] 6 tests from AverageModuleTest 51: [ RUN ] AverageModuleTest.BasicTest 51: [ OK ] AverageModuleTest.BasicTest (0 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipointData 51: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 51: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 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 (2 ms) 51: [----------] 6 tests from AverageModuleTest (4 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 (0 ms) 51: [----------] 2 tests from FrameAverageModuleTest (0 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 (0 ms) 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [----------] 2 tests from SimpleHistogramModuleTest (1 ms total) 51: 51: [----------] 3 tests from WeightedHistogramModuleTest 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 51: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 51: [----------] 3 tests from WeightedHistogramModuleTest (2 ms total) 51: 51: [----------] 3 tests from BinAverageModuleTest 51: [ RUN ] BinAverageModuleTest.ComputesCorrectly 51: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 51: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 51: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 51: [----------] 3 tests from BinAverageModuleTest (1 ms total) 51: 51: [----------] 4 tests from AbstractAverageHistogramTest 51: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 51: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (2 ms) 51: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 51: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 51: [----------] 4 tests from AbstractAverageHistogramTest (4 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 (0 ms) 51: [----------] 3 tests from LifetimeModuleTest (1 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 69 tests from 14 test suites ran. (26 ms total) 51: [ PASSED ] 69 tests. 51/81 Test #51: AnalysisDataUnitTests .......................... Passed 0.16 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 (2 ms) 52: [----------] 1 test from OutputSelectorDeathTest (2 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 (2 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 (1 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 (1 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 (3 ms) 52: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 52: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 52: [----------] 5 tests from TrajectoryFrameWriterTest (9 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 (1 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 (1 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 (1 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 (1 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 (2 ms) 52: [----------] 5 tests from SetAtomsTest (10 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 (1 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 (2 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 (1 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 (1 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 (1 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 (1 ms) 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (11 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 (1 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 (1 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 (1 ms) 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (5 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 (3 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 (3 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 (3 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 (3 ms) 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (15 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 (1 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 (1 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 (1 ms) 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (5 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 (1 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 (1 ms) 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (3 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 (1 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 (1 ms) 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (3 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 (1 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 (1 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 (1 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 (1 ms) 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput (7 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 64 tests from 19 test suites ran. (76 ms total) 52: [ PASSED ] 64 tests. 52/81 Test #52: CoordinateIOTests .............................. Passed 0.22 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 (2 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 11 tests from AngleModuleTest (20 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 (0 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 (0 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 (0 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 (0 ms) 53: [----------] 5 tests from ClustsizeTest (5 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 (1 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 (2 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (4 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 (5 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 (5 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 (1 ms) 53: [----------] 4 tests from ConvertTrjModuleTest (13 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 (1 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 (1 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 (1 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 (4 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 (4 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 (4 ms) 53: [----------] 6 tests from DistanceModuleTest (21 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 (1 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 (1 ms) 53: [----------] 2 tests from ExtractClusterModuleTest (2 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 (48 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 (48 ms) 53: [----------] 2 tests from FreeVolumeModuleTest (97 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 (1 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 (1 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 (1 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 (1 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 -606090513 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 (13 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 -56371554 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 (12 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 -134299657 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 (12 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 -1175916612 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 (12 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 -1347105857 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 (12 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 -7471171 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 (12 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 2130673531 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 (12 ms) 53: [----------] 11 tests from MsdModuleTest (95 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 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 (1 ms) 53: [----------] 9 tests from PairDistanceModuleTest (13 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 (12 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 (8 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 (13 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 (7 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 (14 ms) 53: [----------] 5 tests from RdfModuleTest (57 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 (6 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 (3 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 (3 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 (4 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 (4 ms) 53: [----------] 5 tests from SasaModuleTest (23 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 (2 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 (1 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 (1 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 (1 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 (2 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 (1 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 (1 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 (1 ms) 53: [----------] 8 tests from SelectModuleTest (15 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 (0 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 53: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 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 (0 ms) 53: [ RUN ] SurfaceAreaTest.Computes100Points 53: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 53: [----------] 10 tests from SurfaceAreaTest (5 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 (1 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 (1 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 -7496101 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 (165 ms) 53: [----------] 4 tests from TopologyInformation (169 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 (2 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 (1 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 (1 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 (1 ms) 53: [----------] 4 tests from TrajectoryModuleTest (6 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. (552 ms total) 53: [ PASSED ] 96 tests. 53/81 Test #53: TrajectoryAnalysisUnitTests .................... Passed 0.68 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 (4 ms) 54: [----------] 1 test from DhdlTest (4 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 (6 ms) 54: [----------] 1 test from OriresTest (6 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 (1 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 (1 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 (1 ms) 54: [----------] 3 tests from EnergyTest (4 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 (21 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 (17 ms) 54: [----------] 2 tests from ViscosityTest (38 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 7 tests from 4 test suites ran. (54 ms total) 54: [ PASSED ] 7 tests. 54/81 Test #54: EnergyAnalysisUnitTests ........................ Passed 0.20 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 -540183713 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 = -540183713 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 (6 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 (0 ms) 55: [----------] 2 tests from DumpTest (7 ms total) 55: 55: [----------] 3 tests from HelpwritingTest 55: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 55: [ OK ] HelpwritingTest.ConvertTprWritesHelp (3 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 (3 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 2111814641 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 (0 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 (0 ms) 55: [----------] 4 tests from ReportMethodsTest (0 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 -799025468 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 (161 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 -13442 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 (163 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 -84758685 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 (158 ms) 55: [----------] 3 tests from ConvertTprTest (484 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 (0 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 (0 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 (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 (0 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 (4 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 (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 (0 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 (0 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 (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 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 (0 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 (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 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 (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 (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 (7 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 54 tests from 6 test suites ran. (836 ms total) 55: [ PASSED ] 54 tests. 55/81 Test #55: ToolUnitTests .................................. Passed 1.00 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 (0 ms) 56: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 56: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 56: [----------] 2 tests from FileMD5Test (0 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 (0 ms) 56: [----------] 4 tests from MrcDensityMap (0 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 (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 42 tests from 10 test suites ran. (2 ms total) 56: [ PASSED ] 42 tests. 56/81 Test #56: FileIOTests .................................... Passed 0.14 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 (0 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 (0 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 (7 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 57: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (7 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchBox 57: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 57: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (4 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 57: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 57: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 57: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (20 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 (1 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 57: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 57: [----------] 15 tests from NeighborhoodSearchTest (48 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 (1 ms total) 57: 57: [----------] 33 tests from SelectionCollectionTest 57: [ RUN ] SelectionCollectionTest.HandlesNoSelections 57: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 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 (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 (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 (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 (1 ms) 57: [----------] 33 tests from SelectionCollectionTest (9 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 (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 (3 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 (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 (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 (1 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 (0 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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 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 (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 57: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 57: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 57: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 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 (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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 57: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 57: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 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 (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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 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 (0 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 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (0 ms) 57: [----------] 70 tests from SelectionCollectionDataTest (32 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 (2 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 (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 (1 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 201 tests from 11 test suites ran. (102 ms total) 57: [ PASSED ] 201 tests. 57/81 Test #57: SelectionUnitTests ............................. Passed 0.23 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 (8 ms) 58: [----------] 1 test from MdrunTest (8 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: 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 -1537 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 0.002 194.9 58: (ns/day) (hour/ns) 58: Performance: 104.736 0.229 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 (7 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: 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 -67117187 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: NOTE: 10 % of the run time was spent in pair search, 58: you might want to increase nstlist (this has no effect on accuracy) 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.001 0.001 190.1 58: (ns/day) (hour/ns) 58: Performance: 244.114 0.098 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 (4 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: 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 1601174009 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: 0.001 0.001 187.7 58: (ns/day) (hour/ns) 58: Performance: 294.385 0.082 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 (4 ms) 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (16 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: 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: 0.001 0.001 190.7 58: (ns/day) (hour/ns) 58: Performance: 2228.869 0.011 58: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (4 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: 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: 0.002 0.001 194.2 58: (ns/day) (hour/ns) 58: Performance: 1641.949 0.015 58: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (5 ms) 58: [----------] 2 tests from Argon12/OutputFiles (9 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: 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 -274727957 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: 0.009 0.005 197.7 58: (ns/day) (hour/ns) 58: Performance: 132.389 0.181 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (9 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: 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 -29364273 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: 0.036 0.018 199.4 58: (ns/day) (hour/ns) 58: Performance: 33.371 0.719 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (26 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: 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 -201592905 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: 0.002 0.001 193.3 58: (ns/day) (hour/ns) 58: Performance: 469.154 0.051 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (5 ms) 58: [----------] 3 tests from MdrunCanWrite/Trajectories (40 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: 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 -56807425 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 0.002 194.1 58: (ns/day) (hour/ns) 58: Performance: 169.103 0.142 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (6 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: 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 -18301089 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: 0.001 0.001 188.6 58: (ns/day) (hour/ns) 58: Performance: 382.266 0.063 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (4 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: 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 -1218527811 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: 0.002 0.001 191.6 58: (ns/day) (hour/ns) 58: Performance: 273.983 0.088 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (4 ms) 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories (16 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 12 tests from 5 test suites ran. (107 ms total) 58: [ PASSED ] 12 tests. 58/81 Test #58: MdrunOutputTests ............................... Passed 0.26 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: 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 = 4.5099888e+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 -93331602 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 (4 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 59: Number of degrees of freedom in T-Coupling group rest is 33.00 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 = -9.8207725e+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 -138486533 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 (4 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: 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 = -1.0954997e+04 59: Maximum force = 7.4724795e+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 1576204277 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 (3 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: 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 = 4.5099888e+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 2078005237 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 (3 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 59: Number of degrees of freedom in T-Coupling group rest is 33.00 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 528609278 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 (3 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: 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 -67108865 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: 0.003 0.001 194.9 59: (ns/day) (hour/ns) 59: Performance: 182.318 0.132 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: 0.003 0.001 192.4 59: (ns/day) (hour/ns) 59: Performance: 314.956 0.076 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 (8 ms) 59: [----------] 9 tests from DensityFittingTest (29 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: 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: 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: 0.000 0.000 186.0 59: (ns/day) (hour/ns) 59: Performance: 470.634 0.051 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 2138832766 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 (4 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: 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: 0.000 0.000 187.3 59: (ns/day) (hour/ns) 59: Performance: 417.017 0.058 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 -402849835 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 (4 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: 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: 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: 0.000 0.000 186.2 59: (ns/day) (hour/ns) 59: Performance: 489.052 0.049 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 -562298913 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 (3 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: 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: NOTE: 15 % 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 0.000 190.8 59: (ns/day) (hour/ns) 59: Performance: 316.220 0.076 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 -235013331 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 (10 ms) 59: [----------] 4 tests from MimicTest (22 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: 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 54169. 59: IMD: -imdwait not set, starting simulation. 59: starting mdrun 'Glycine' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to -540737 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: 0.004 0.002 195.5 59: (ns/day) (hour/ns) 59: Performance: 275.371 0.087 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (59 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: 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 41397. 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 = 1.1977061e+03 59: Maximum force = 1.7794875e+04 on atom 9 59: Norm of force = 7.8732895e+03 59: Setting the LD random seed to -673448034 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 (54 ms) 59: [----------] 2 tests from WithIntegrator/ImdTest (113 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 15 tests from 3 test suites ran. (177 ms total) 59: [ PASSED ] 15 tests. 59/81 Test #59: MdrunModulesTests .............................. Passed 0.32 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 -1007313442 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 (2 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 -68597761 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 (2 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 -134296578 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 (2 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 -1083310721 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 (5 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 -37912641 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 (6 ms) 60: [----------] 5 tests from GromppTest (19 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: 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 -808654865 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: 0.015 0.008 198.5 60: (ns/day) (hour/ns) 60: Performance: 34.020 0.705 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: 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: Core t (s) Wall t (s) (%) 60: Time: 0.001 0.001 165.0 60: (ns/day) (hour/ns) 60: Performance: 322.888 0.074 60: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (15 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: 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 8: Run time exceeded 0.000 hours, will terminate the run within 2 steps 60: Setting the LD random seed to 2113142261 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: 20 % 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 0.001 171.2 60: (ns/day) (hour/ns) 60: Performance: 883.011 0.027 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: 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 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: 0.004 0.002 184.9 60: (ns/day) (hour/ns) 60: Performance: 4132.030 0.006 60: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (12 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: 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 -14401 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: 0.001 0.001 188.2 60: (ns/day) (hour/ns) 60: Performance: 415.265 0.058 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: 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 0.001 194.4 60: (ns/day) (hour/ns) 60: Performance: 241.914 0.099 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: 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 0.001 194.7 60: (ns/day) (hour/ns) 60: Performance: 275.092 0.087 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: 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: 0.001 0.001 147.5 60: (ns/day) (hour/ns) 60: Performance: 451.292 0.053 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: 14 % 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 0.000 179.7 60: (ns/day) (hour/ns) 60: Performance: 391.348 0.061 60: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (22 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: 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 -42125 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 0.001 192.6 60: (ns/day) (hour/ns) 60: Performance: 275.162 0.087 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: 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 0.001 192.7 60: (ns/day) (hour/ns) 60: Performance: 443.668 0.054 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (7 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: 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 -941794118 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: 0.005 0.003 195.5 60: (ns/day) (hour/ns) 60: Performance: 97.016 0.247 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 (6 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: 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 -341311771 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: 0.004 0.002 196.3 60: (ns/day) (hour/ns) 60: Performance: 124.990 0.192 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: 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: NOTE: 14 % 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: 0.024 0.012 199.5 60: (ns/day) (hour/ns) 60: Performance: 21.771 1.102 60: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (20 ms) 60: [----------] 6 tests from MdrunTerminationTest (86 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: 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: 0.002 0.001 193.4 60: (ns/day) (hour/ns) 60: Performance: 1504.051 0.016 60: trr version: GMX_trn_file (single precision) 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (4 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: 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: 0.070 0.035 199.8 60: (ns/day) (hour/ns) 60: Performance: 42.168 0.569 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (39 ms) 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (44 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: 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: 0.001 0.001 186.7 60: (ns/day) (hour/ns) 60: Performance: 2280.857 0.011 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: 0.001 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 1544.266 0.016 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: 0.002 0.001 192.6 60: (ns/day) (hour/ns) 60: Performance: 929.464 0.026 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: 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_secondpart.part0002.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 (9 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: 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: 0.002 0.001 194.5 60: (ns/day) (hour/ns) 60: Performance: 1647.218 0.015 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: 0.001 0.001 193.9 60: (ns/day) (hour/ns) 60: Performance: 1161.086 0.021 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: Core t (s) Wall t (s) (%) 60: Time: 0.001 0.001 189.8 60: (ns/day) (hour/ns) 60: Performance: 1104.093 0.022 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: 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_secondpart.part0002.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 (12 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: 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: 0.001 0.001 191.7 60: (ns/day) (hour/ns) 60: Performance: 2546.752 0.009 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: 0.001 0.001 190.7 60: (ns/day) (hour/ns) 60: Performance: 1502.991 0.016 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: 0.001 0.000 190.2 60: (ns/day) (hour/ns) 60: Performance: 1601.911 0.015 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: 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_secondpart.part0002.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 (8 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: 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: 0.001 0.001 191.4 60: (ns/day) (hour/ns) 60: Performance: 2536.267 0.009 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: 0.001 0.001 190.6 60: (ns/day) (hour/ns) 60: Performance: 1426.100 0.017 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: 0.001 0.000 190.3 60: (ns/day) (hour/ns) 60: Performance: 1628.303 0.015 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: 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_secondpart.part0002.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 (8 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: 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: 0.001 0.001 191.6 60: (ns/day) (hour/ns) 60: Performance: 1995.011 0.012 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: 0.001 0.001 188.5 60: (ns/day) (hour/ns) 60: Performance: 1512.050 0.016 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: 0.002 0.001 193.9 60: (ns/day) (hour/ns) 60: Performance: 748.048 0.032 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: 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_secondpart.part0002.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 (10 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: 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: 0.002 0.001 194.4 60: (ns/day) (hour/ns) 60: Performance: 1586.964 0.015 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: 0.002 0.001 195.1 60: (ns/day) (hour/ns) 60: Performance: 870.892 0.028 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: 0.001 0.001 191.5 60: (ns/day) (hour/ns) 60: Performance: 1067.941 0.022 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: 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_secondpart.part0002.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 (10 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: 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: 0.002 0.001 192.6 60: (ns/day) (hour/ns) 60: Performance: 1881.672 0.013 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: 0.001 0.000 189.4 60: (ns/day) (hour/ns) 60: Performance: 1555.313 0.015 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: 0.002 0.001 193.0 60: (ns/day) (hour/ns) 60: Performance: 936.941 0.026 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 192.4 60: (ns/day) (hour/ns) 60: Performance: 2016.561 0.012 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: 0.001 0.001 189.6 60: (ns/day) (hour/ns) 60: Performance: 1376.737 0.017 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: 0.002 0.001 194.5 60: (ns/day) (hour/ns) 60: Performance: 708.712 0.034 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: 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_secondpart.part0002.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 (10 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: 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: 0.004 0.002 190.2 60: (ns/day) (hour/ns) 60: Performance: 723.499 0.033 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: 0.004 0.002 191.9 60: (ns/day) (hour/ns) 60: Performance: 391.489 0.061 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: 0.003 0.002 190.7 60: (ns/day) (hour/ns) 60: Performance: 451.855 0.053 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: 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_secondpart.part0002.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 (28 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: 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: 0.004 0.002 195.0 60: (ns/day) (hour/ns) 60: Performance: 754.143 0.032 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: 0.002 0.001 191.8 60: (ns/day) (hour/ns) 60: Performance: 700.944 0.034 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: 0.002 0.001 191.7 60: (ns/day) (hour/ns) 60: Performance: 667.244 0.036 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: 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_secondpart.part0002.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 (34 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: 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: 0.004 0.002 195.5 60: (ns/day) (hour/ns) 60: Performance: 712.043 0.034 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: 0.002 0.001 193.0 60: (ns/day) (hour/ns) 60: Performance: 651.386 0.037 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: 0.002 0.001 192.4 60: (ns/day) (hour/ns) 60: Performance: 708.096 0.034 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: 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_secondpart.part0002.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 (33 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: 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: 0.004 0.002 196.2 60: (ns/day) (hour/ns) 60: Performance: 684.434 0.035 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: 0.002 0.001 194.0 60: (ns/day) (hour/ns) 60: Performance: 639.132 0.038 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: 0.002 0.001 193.4 60: (ns/day) (hour/ns) 60: Performance: 681.322 0.035 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: 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_secondpart.part0002.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 (30 ms) 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (209 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: 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: 0.003 0.002 194.0 60: (ns/day) (hour/ns) 60: Performance: 864.402 0.028 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: 0.002 0.001 191.4 60: (ns/day) (hour/ns) 60: Performance: 663.039 0.036 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: 0.002 0.001 190.7 60: (ns/day) (hour/ns) 60: Performance: 796.651 0.030 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: 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_secondpart.part0002.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 (22 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: 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: 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: 0.033 0.016 199.6 60: (ns/day) (hour/ns) 60: Performance: 90.086 0.266 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: 0.003 0.001 195.6 60: (ns/day) (hour/ns) 60: Performance: 569.494 0.042 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: 0.003 0.001 190.3 60: (ns/day) (hour/ns) 60: Performance: 588.186 0.041 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: 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_secondpart.part0002.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 (41 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: 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: 0.005 0.003 195.7 60: (ns/day) (hour/ns) 60: Performance: 564.312 0.043 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: 0.003 0.001 193.1 60: (ns/day) (hour/ns) 60: Performance: 579.409 0.041 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: 0.002 0.001 191.2 60: (ns/day) (hour/ns) 60: Performance: 793.550 0.030 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: 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_secondpart.part0002.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 (35 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: 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: 0.003 0.002 195.0 60: (ns/day) (hour/ns) 60: Performance: 820.975 0.029 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: 0.002 0.001 191.7 60: (ns/day) (hour/ns) 60: Performance: 724.132 0.033 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: 0.003 0.001 193.5 60: (ns/day) (hour/ns) 60: Performance: 554.487 0.043 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: 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_secondpart.part0002.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 (31 ms) 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (131 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: 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: 0.001 0.001 190.7 60: (ns/day) (hour/ns) 60: Performance: 2164.650 0.011 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: 0.004 0.002 194.7 60: (ns/day) (hour/ns) 60: Performance: 401.760 0.060 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: 0.002 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 957.291 0.025 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: 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_secondpart.part0002.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 (16 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: 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: 0.008 0.004 197.4 60: (ns/day) (hour/ns) 60: Performance: 381.013 0.063 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: 0.004 0.002 194.9 60: (ns/day) (hour/ns) 60: Performance: 363.559 0.066 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: 14 % 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: 0.025 0.012 199.4 60: (ns/day) (hour/ns) 60: Performance: 63.212 0.380 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: 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_secondpart.part0002.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 (34 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: 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: 0.001 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 2331.792 0.010 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: 0.002 0.001 192.3 60: (ns/day) (hour/ns) 60: Performance: 701.547 0.034 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: 0.001 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 1431.734 0.017 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: 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_secondpart.part0002.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 (11 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: 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: 0.002 0.001 194.8 60: (ns/day) (hour/ns) 60: Performance: 1772.833 0.014 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: 0.002 0.001 194.8 60: (ns/day) (hour/ns) 60: Performance: 660.756 0.036 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: 0.002 0.001 189.6 60: (ns/day) (hour/ns) 60: Performance: 828.210 0.029 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: 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_secondpart.part0002.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 (13 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: 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: NOTE: 42 % 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: 0.004 0.002 196.9 60: (ns/day) (hour/ns) 60: Performance: 729.928 0.033 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: 0.001 0.001 192.9 60: (ns/day) (hour/ns) 60: Performance: 1062.029 0.023 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: 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: 0.022 0.011 198.6 60: (ns/day) (hour/ns) 60: Performance: 70.036 0.343 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: 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_secondpart.part0002.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 (26 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: 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: 0.003 0.001 195.4 60: (ns/day) (hour/ns) 60: Performance: 1026.423 0.023 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: 0.002 0.001 193.9 60: (ns/day) (hour/ns) 60: Performance: 632.194 0.038 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: 0.002 0.001 189.5 60: (ns/day) (hour/ns) 60: Performance: 605.100 0.040 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: 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_secondpart.part0002.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 (15 ms) 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (117 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: 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: 0.003 0.002 193.4 60: (ns/day) (hour/ns) 60: Performance: 924.320 0.026 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: 0.001 0.001 188.0 60: (ns/day) (hour/ns) 60: Performance: 1154.919 0.021 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: 0.004 0.002 194.7 60: (ns/day) (hour/ns) 60: Performance: 407.228 0.059 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: 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_secondpart.part0002.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 (17 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: 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: 0.001 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 1919.188 0.013 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: 0.001 0.001 188.6 60: (ns/day) (hour/ns) 60: Performance: 1407.635 0.017 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: 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: 0.009 0.004 197.8 60: (ns/day) (hour/ns) 60: Performance: 179.905 0.133 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: 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_secondpart.part0002.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 (17 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: 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: 0.002 0.001 194.4 60: (ns/day) (hour/ns) 60: Performance: 1576.406 0.015 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: 0.002 0.001 194.3 60: (ns/day) (hour/ns) 60: Performance: 952.816 0.025 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: 0.001 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 989.230 0.024 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: 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_secondpart.part0002.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 (10 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: 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: 0.002 0.001 194.4 60: (ns/day) (hour/ns) 60: Performance: 1185.413 0.020 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: 0.002 0.001 194.4 60: (ns/day) (hour/ns) 60: Performance: 885.793 0.027 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: 0.002 0.001 189.2 60: (ns/day) (hour/ns) 60: Performance: 882.677 0.027 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: 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_secondpart.part0002.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 (11 ms) 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (56 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: 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: 0.005 0.003 196.4 60: (ns/day) (hour/ns) 60: Performance: 537.245 0.045 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: 0.001 0.001 188.5 60: (ns/day) (hour/ns) 60: Performance: 1392.015 0.017 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: 0.002 0.001 191.6 60: (ns/day) (hour/ns) 60: Performance: 781.570 0.031 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: 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_secondpart.part0002.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 (12 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: 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: 0.001 0.001 190.1 60: (ns/day) (hour/ns) 60: Performance: 2069.397 0.012 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: 0.002 0.001 191.8 60: (ns/day) (hour/ns) 60: Performance: 675.957 0.036 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: 0.001 0.001 188.7 60: (ns/day) (hour/ns) 60: Performance: 1349.396 0.018 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: 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_secondpart.part0002.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 (12 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: 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: 0.001 0.001 190.4 60: (ns/day) (hour/ns) 60: Performance: 2072.878 0.012 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: 0.001 0.001 188.4 60: (ns/day) (hour/ns) 60: Performance: 1328.509 0.018 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: 0.001 0.001 189.5 60: (ns/day) (hour/ns) 60: Performance: 1218.793 0.020 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 190.4 60: (ns/day) (hour/ns) 60: Performance: 2079.876 0.012 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: 0.001 0.001 190.1 60: (ns/day) (hour/ns) 60: Performance: 1164.818 0.021 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: 0.001 0.001 183.3 60: (ns/day) (hour/ns) 60: Performance: 1285.063 0.019 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 190.7 60: (ns/day) (hour/ns) 60: Performance: 2101.874 0.011 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: 0.001 0.001 188.4 60: (ns/day) (hour/ns) 60: Performance: 1364.070 0.018 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: 0.001 0.001 188.5 60: (ns/day) (hour/ns) 60: Performance: 1355.002 0.018 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: 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_secondpart.part0002.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 (9 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: 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: 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: 0.004 0.002 196.1 60: (ns/day) (hour/ns) 60: Performance: 695.876 0.034 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: 0.001 0.001 188.4 60: (ns/day) (hour/ns) 60: Performance: 1316.179 0.018 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: 0.002 0.001 190.9 60: (ns/day) (hour/ns) 60: Performance: 870.660 0.028 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: 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_secondpart.part0002.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 (14 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: 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: 0.001 0.001 152.8 60: (ns/day) (hour/ns) 60: Performance: 1704.175 0.014 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: NOTE: 14 % 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: 0.001 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 1154.101 0.021 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: 0.002 0.001 191.0 60: (ns/day) (hour/ns) 60: Performance: 949.488 0.025 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 190.5 60: (ns/day) (hour/ns) 60: Performance: 2101.874 0.011 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: 0.001 0.001 191.4 60: (ns/day) (hour/ns) 60: Performance: 992.239 0.024 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: 0.001 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 1356.129 0.018 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: 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_secondpart.part0002.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 (10 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: 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: 0.001 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 2077.772 0.012 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: 0.001 0.001 188.4 60: (ns/day) (hour/ns) 60: Performance: 1408.243 0.017 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: 0.001 0.001 189.3 60: (ns/day) (hour/ns) 60: Performance: 1408.243 0.017 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: 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_secondpart.part0002.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 (9 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: 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: 0.002 0.001 194.8 60: (ns/day) (hour/ns) 60: Performance: 1265.789 0.019 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: 0.001 0.001 192.8 60: (ns/day) (hour/ns) 60: Performance: 1010.375 0.024 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: 0.002 0.001 187.2 60: (ns/day) (hour/ns) 60: Performance: 962.944 0.025 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: 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_secondpart.part0002.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 (11 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: 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: NOTE: 51 % 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: 0.005 0.003 197.6 60: (ns/day) (hour/ns) 60: Performance: 530.857 0.045 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: 0.002 0.001 192.0 60: (ns/day) (hour/ns) 60: Performance: 909.760 0.026 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: 0.002 0.001 186.9 60: (ns/day) (hour/ns) 60: Performance: 925.771 0.026 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: 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_secondpart.part0002.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 (12 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: 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: 0.002 0.001 194.3 60: (ns/day) (hour/ns) 60: Performance: 1555.705 0.015 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: 0.002 0.001 192.3 60: (ns/day) (hour/ns) 60: Performance: 961.808 0.025 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: 0.002 0.001 189.3 60: (ns/day) (hour/ns) 60: Performance: 628.176 0.038 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: 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_secondpart.part0002.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 (13 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: 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: 0.002 0.001 194.5 60: (ns/day) (hour/ns) 60: Performance: 1484.123 0.016 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: 0.002 0.001 192.0 60: (ns/day) (hour/ns) 60: Performance: 962.376 0.025 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: 0.002 0.001 185.3 60: (ns/day) (hour/ns) 60: Performance: 886.034 0.027 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: 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_secondpart.part0002.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 (11 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: 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: 0.002 0.001 194.3 60: (ns/day) (hour/ns) 60: Performance: 1523.768 0.016 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: 0.002 0.001 192.5 60: (ns/day) (hour/ns) 60: Performance: 936.403 0.026 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: 0.002 0.001 190.0 60: (ns/day) (hour/ns) 60: Performance: 652.951 0.037 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: 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_secondpart.part0002.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 (11 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: 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: 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: 0.015 0.008 199.0 60: (ns/day) (hour/ns) 60: Performance: 194.918 0.123 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: 0.002 0.001 192.5 60: (ns/day) (hour/ns) 60: Performance: 856.034 0.028 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: 0.002 0.001 187.9 60: (ns/day) (hour/ns) 60: Performance: 951.149 0.025 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: 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_secondpart.part0002.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 (19 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: 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: 0.002 0.001 195.2 60: (ns/day) (hour/ns) 60: Performance: 1281.055 0.019 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: 0.003 0.001 194.9 60: (ns/day) (hour/ns) 60: Performance: 573.499 0.042 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: 0.002 0.001 189.1 60: (ns/day) (hour/ns) 60: Performance: 913.583 0.026 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: 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_secondpart.part0002.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 (11 ms) 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (192 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: 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: 0.003 0.001 195.2 60: (ns/day) (hour/ns) 60: Performance: 1067.879 0.022 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: 0.003 0.002 194.7 60: (ns/day) (hour/ns) 60: Performance: 477.384 0.050 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: 0.002 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 670.123 0.036 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: 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_secondpart.part0002.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 (13 ms) 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (13 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: 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: 0.008 0.004 197.0 60: (ns/day) (hour/ns) 60: Performance: 381.154 0.063 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: 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: 0.020 0.010 199.1 60: (ns/day) (hour/ns) 60: Performance: 76.608 0.313 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: NOTE: 26 % 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: 0.003 0.001 192.9 60: (ns/day) (hour/ns) 60: Performance: 536.518 0.045 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: 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_secondpart.part0002.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 (29 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: 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: NOTE: 46 % 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: 0.007 0.004 197.8 60: (ns/day) (hour/ns) 60: Performance: 408.203 0.059 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: 0.002 0.001 193.0 60: (ns/day) (hour/ns) 60: Performance: 872.523 0.028 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: 0.002 0.001 189.3 60: (ns/day) (hour/ns) 60: Performance: 838.214 0.029 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: 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_secondpart.part0002.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 (15 ms) 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (44 ms total) 60: 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: Setting the AWH bias MC random seed to -1346765511 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 -1243762691 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: 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: 0.006 0.003 193.4 60: (ns/day) (hour/ns) 60: Performance: 467.633 0.051 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: 0.003 0.001 188.7 60: (ns/day) (hour/ns) 60: Performance: 549.906 0.044 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: 0.004 0.002 191.7 60: (ns/day) (hour/ns) 60: Performance: 385.519 0.062 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: 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_secondpart.part0002.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 (34 ms) 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: Setting the AWH bias MC random seed to 1458298655 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 -169362753 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: 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: 0.004 0.002 193.1 60: (ns/day) (hour/ns) 60: Performance: 710.564 0.034 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: 0.003 0.001 188.7 60: (ns/day) (hour/ns) 60: Performance: 580.853 0.041 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: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.2 60: (ns/day) (hour/ns) 60: Performance: 467.396 0.051 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: 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_secondpart.part0002.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 (34 ms) 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (68 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: 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: 0.007 0.003 197.6 60: (ns/day) (hour/ns) 60: Performance: 445.548 0.054 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: 0.004 0.002 195.9 60: (ns/day) (hour/ns) 60: Performance: 354.087 0.068 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: 0.005 0.002 190.8 60: (ns/day) (hour/ns) 60: Performance: 328.547 0.073 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: 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_secondpart.part0002.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 (38 ms) 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (38 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: 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 -1210146834 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 0.001 187.9 60: (ns/day) (hour/ns) 60: Performance: 159.889 0.150 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 (5 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: 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 -178717777 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: 0.001 0.001 192.1 60: (ns/day) (hour/ns) 60: Performance: 247.956 0.097 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 (4 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: 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 1072756091 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: 0.001 0.001 187.9 60: (ns/day) (hour/ns) 60: Performance: 269.634 0.089 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 (4 ms) 60: [----------] 3 tests from Checking/InitialConstraintsTest (14 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 66 tests from 13 test suites ran. (1088 ms total) 60: [ PASSED ] 66 tests. 60/81 Test #60: MdrunIOTests ................................... Passed 1.21 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 1207885751 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: 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: 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/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: 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: 39 % 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: 0.267 0.134 199.9 61: (ns/day) (hour/ns) 61: Performance: 9.700 2.474 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: 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: 0.193 0.097 199.9 61: (ns/day) (hour/ns) 61: Performance: 13.411 1.790 61: [ OK ] CompelTest.SwapCanRun (481 ms) 61: [----------] 1 test from CompelTest (481 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 -1078150321 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_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: This run will generate roughly 0 Mb of data 61: 61: There were 3 notes 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: 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: 0.000 0.000 189.7 61: (ns/day) (hour/ns) 61: Performance: 373.981 0.064 61: [ OK ] BondedInteractionsTest.NormalBondWorks (3 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 -1092433 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: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 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: This run will generate roughly 0 Mb of data 61: 61: There were 3 notes 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 [ OK ] BondedInteractionsTest.TabulatedBondWorks (4 ms) 61: 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: 0.000 0.000 183.2 61: (ns/day) (hour/ns) 61: Performance: 342.198 0.070 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 -110760713 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: 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 [ OK ] BondedInteractionsTest.NormalAngleWorks (3 ms) 61: Last frame 0 time 0.000 61: 61: NOTE: 21 % 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: 0.000 0.000 186.5 61: (ns/day) (hour/ns) 61: Performance: 349.795 0.069 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 2113551983 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 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/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: This run will generate roughly 0 Mb of data 61: 61: There were 3 notes 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: 21 % 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: 0.000 0.000 189.3 61: (ns/day) (hour/ns) 61: Performance: 402.653 0.060 61: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (4 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 -1343359490 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: This run will generate roughly 0 Mb of data 61: 61: There were 3 notes 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: 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: 0.000 0.000 190.2 61: (ns/day) (hour/ns) 61: Performance: 355.631 0.067 61: [ OK ] BondedInteractionsTest.NormalDihedralWorks (3 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: Setting the LD random seed to -822648836 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 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/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: This run will generate roughly 0 Mb of data 61: 61: There were 3 notes 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 [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (4 ms) 61: 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: 0.000 0.000 188.2 61: (ns/day) (hour/ns) 61: Performance: 355.282 0.068 61: [----------] 6 tests from BondedInteractionsTest (24 ms total) 61: 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 61: Setting the LD random seed to -344331267 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 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: 0.95 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: 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: 0.005 0.003 196.4 61: (ns/day) (hour/ns) 61: Performance: 164.527 0.146 61: Setting the LD random seed to -587801217 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 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: 0.95 61: 61: This run will generate roughly 0 Mb of data 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/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: 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: 0.004 0.002 195.6 61: (ns/day) (hour/ns) 61: Performance: 208.845 0.115 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 (23086 ms) 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 61: Setting the LD random seed to 1541631707 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: 0.95 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: This run will generate roughly 0 Mb of data 61: 61: There were 2 notes 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: Setting the LD random seed to -671744007 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.005 0.002 196.2 61: (ns/day) (hour/ns) 61: Performance: 182.526 0.131 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: 0.95 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: This run will generate roughly 0 Mb of data 61: 61: There were 2 notes 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: 0.004 0.002 195.6 61: (ns/day) (hour/ns) 61: Performance: 226.153 0.106 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (23 ms) 61: 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_sim1.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_sim2.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 [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (23110 ms total) 61: 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 61: Setting the LD random seed to -613712193 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: 61: This run will generate roughly 0 Mb of data 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: 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: 0.002 0.001 189.6 61: (ns/day) (hour/ns) 61: Performance: 540.071 0.044 61: Setting the LD random seed to -1073772033 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: 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: This run will generate roughly 0 Mb of data 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: [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (9 ms) 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (9 ms total) 61: 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.002 0.001 190.3 61: (ns/day) (hour/ns) 61: Performance: 494.930 0.048 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: 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: Reading energy frame 0 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_sim1.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_sim2.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 [ 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: 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_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: 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: 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: 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: 0.002 0.001 190.9 61: (ns/day) (hour/ns) 61: Performance: 679.902 0.035 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: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (9 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generating 1-4 interactions: fudge = 0.5 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: 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: 0.002 0.001 191.9 61: (ns/day) (hour/ns) 61: Performance: 695.266 0.035 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (9 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: 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: 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: 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: 0.003 0.001 193.6 61: (ns/day) (hour/ns) 61: Performance: 577.562 0.042 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (9 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: 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: 0.003 0.001 193.8 61: (ns/day) (hour/ns) 61: Performance: 549.906 0.044 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (12 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: 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: 0.003 0.001 193.8 61: (ns/day) (hour/ns) 61: Performance: 600.643 0.040 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (10 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 61: 61: 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: 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_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: There were 4 notes 61: 61: There was 1 warning 61: 61: This run will generate roughly 0 Mb of data 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: 0.002 0.001 193.6 61: (ns/day) (hour/ns) 61: Performance: 652.168 0.037 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (11 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: 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_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: 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: This run will generate roughly 0 Mb of data 61: 61: There were 4 notes 61: 61: There was 1 warning 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: 0.003 0.001 193.2 61: (ns/day) (hour/ns) 61: Performance: 580.853 0.041 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (11 ms) 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest (73 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 -859046419 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: 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: 0.002 0.001 192.3 61: (ns/day) (hour/ns) 61: Performance: 1684.219 0.014 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (4 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: 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: Setting gen_seed to 1173202935 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: 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: 0.001 0.001 190.9 61: (ns/day) (hour/ns) 61: Performance: 1989.927 0.012 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (4 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: 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 -273154227 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: 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 (4 ms) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.002 0.001 192.4 61: (ns/day) (hour/ns) 61: Performance: 1559.403 0.015 61: 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 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: 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: Setting gen_seed to -11051 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: 61: There were 2 notes 61: This run will generate roughly 0 Mb of data 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: 61: Core t (s) Wall t (s) (%) 61: Time: 0.002 0.001 192.7 61: (ns/day) (hour/ns) 61: Performance: 1609.818 0.015 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (4 ms) 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (18 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 22 tests from 6 test suites ran. (23765 ms total) 61: [ PASSED ] 21 tests. 61: [ SKIPPED ] 1 test, listed below: 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61/81 Test #61: MdrunTestsOneRank .............................. Passed 23.89 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 -176754697 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: 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: 1.2%. 62: The balanceable part of the MD step is 22%, 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: 6 % of the run time was spent in domain decomposition, 62: 33 % 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: 0.375 0.094 399.6 62: (ns/day) (hour/ns) 62: Performance: 13.817 1.737 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: 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: 0.265 0.066 399.5 62: (ns/day) (hour/ns) 62: Performance: 19.554 1.227 62: [ OK ] CompelTest.SwapCanRun (432 ms) 62: [----------] 1 test from CompelTest (432 ms total) 62: 62: [----------] 6 tests from BondedInteractionsTest 62: [ RUN ] BondedInteractionsTest.NormalBondWorks 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: Setting the LD random seed to -1711278081 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_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/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: 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 [ OK ] BondedInteractionsTest.NormalBondWorks (4 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 62: Last frame 0 time 0.000 62: 62: NOTE: 29 % 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: 0.001 0.000 378.5 62: (ns/day) (hour/ns) 62: Performance: 268.933 0.089 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: 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: There were 3 notes 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: Setting the LD random seed to 1023137395 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: 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: 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 0.000 380.4 62: (ns/day) (hour/ns) 62: Performance: 203.760 0.118 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: 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: 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: [ OK ] BondedInteractionsTest.TabulatedBondWorks (4 ms) 62: [ RUN ] BondedInteractionsTest.NormalAngleWorks 62: Setting the LD random seed to -68296713 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: 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.NormalAngleWorks (3 ms) 62: Last frame 0 time 0.000 62: 62: NOTE: 26 % 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: 0.001 0.000 377.0 62: (ns/day) (hour/ns) 62: Performance: 265.680 0.090 62: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 62: Setting the LD random seed to -1839623 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: 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: 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 [ OK ] BondedInteractionsTest.TabulatedAngleWorks (4 ms) 62: Last frame 0 time 0.000 62: 62: NOTE: 29 % 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: Core t (s) Wall t (s) (%) 62: Time: 0.001 0.000 377.8 62: (ns/day) (hour/ns) 62: Performance: 266.462 0.090 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 -229150849 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 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/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: This run will generate roughly 0 Mb of data 62: 62: There were 3 notes 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 Last frame 0 time 0.000 62: 62: NOTE: 24 % 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: 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: 0.002 0.000 382.8 62: (ns/day) (hour/ns) 62: Performance: 207.791 0.116 62: [ OK ] BondedInteractionsTest.NormalDihedralWorks (4 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 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 2012872063 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: 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 [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (5 ms) 62: Last frame 0 time 0.000 62: 62: NOTE: 27 % 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: 0.001 0.000 379.1 62: (ns/day) (hour/ns) 62: Performance: 222.802 0.108 62: [----------] 6 tests from BondedInteractionsTest (27 ms total) 62: 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 62: Setting the LD random seed to -881918085 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 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: 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: 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: 0.95 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: 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: 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: 0.010 0.002 390.3 62: (ns/day) (hour/ns) 62: Performance: 176.284 0.136 62: Setting the LD random seed to 766737263 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: 0.95 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: 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: 14 % 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 0.002 388.5 62: (ns/day) (hour/ns) 62: Performance: 206.689 0.116 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: 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: 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 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 0 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 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: trr version: GMX_trn_file (single precision) 62: 62: 62: 62: 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: 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: 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 0 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: Reading energy frame 0 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 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (23172 ms) 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 62: Setting the LD random seed to -402672769 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: 0.95 62: 62: This run will generate roughly 0 Mb of data 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/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: 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: Setting the LD random seed to -344219 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: 0.010 0.003 390.0 62: (ns/day) (hour/ns) 62: Performance: 170.712 0.141 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 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: 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: 0.95 62: 62: This run will generate roughly 0 Mb of data 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/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: 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: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (25 ms) 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (23198 ms total) 62: 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 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 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/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 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: NOTE: 15 % 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 0.002 388.2 62: (ns/day) (hour/ns) 62: Performance: 200.647 0.120 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 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/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 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 ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 62: Setting the LD random seed to -604053767 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: 62: This run will generate roughly 0 Mb of data 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: 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: 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: 0.004 0.001 361.6 62: (ns/day) (hour/ns) 62: Performance: 402.072 0.060 62: Setting the LD random seed to -1627553801 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: 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: 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: 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_sim2.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/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_sim2.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: NOTE: 10 % 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: 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: 0.005 0.001 377.5 62: (ns/day) (hour/ns) 62: Performance: 357.138 0.067 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_sim2.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/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_sim2.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 (12 ms) 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (12 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/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: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 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: 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: This run will generate roughly 0 Mb of data 62: 62: There were 5 notes 62: 62: There was 1 warning 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: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 4.8%. 62: The balanceable part of the MD step is 59%, 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: 13 % 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: 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: 0.006 0.002 384.0 62: (ns/day) (hour/ns) 62: Performance: 489.897 0.049 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (10 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: 62: Generating 1-4 interactions: fudge = 0.5 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: 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: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (11 ms) 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: 3.2%. 62: The balanceable part of the MD step is 60%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 1.9%. 62: 62: 62: NOTE: 13 % 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: 19 % 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 0.002 378.3 62: (ns/day) (hour/ns) 62: Performance: 439.376 0.055 62: 62: 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: 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: This run will generate roughly 0 Mb of data 62: 62: There were 5 notes 62: 62: There was 1 warning 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: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (12 ms) 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 61%, 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: 13 % 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: 19 % 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 0.002 386.1 62: (ns/day) (hour/ns) 62: Performance: 416.511 0.058 62: 62: 62: 62: 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (0 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 62: Generated 2145 of the 2145 non-bonded parameter combinations 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: 62: Generating 1-4 interactions: fudge = 0.5 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: 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: This run will generate roughly 0 Mb of data 62: 62: There were 4 notes 62: 62: There was 1 warning 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: 62: 62: NOTE: 19 % 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 0.002 384.6 62: (ns/day) (hour/ns) 62: Performance: 437.755 0.055 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (12 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: 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: Generating 1-4 interactions: fudge = 0.5 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: 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: 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: 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: starting mdrun 'Alanine-dipeptide' 62: 8 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: 0.007 0.002 386.9 62: (ns/day) (hour/ns) 62: Performance: 430.361 0.056 62: 62: 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (11 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: 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_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: This run will generate roughly 0 Mb of data 62: 62: There were 4 notes 62: 62: There was 1 warning 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: 19 % 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: 0.006 0.001 383.5 62: (ns/day) (hour/ns) 62: Performance: 540.922 0.044 62: 62: 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (12 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: 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_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: 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: This run will generate roughly 0 Mb of data 62: 62: There were 4 notes 62: 62: There was 1 warning 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: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (12 ms) 62: 62: 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: 0.006 0.001 383.0 62: (ns/day) (hour/ns) 62: Performance: 520.880 0.046 62: 62: 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest (85 ms total) 62: 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 62: Generated 3 of the 3 non-bonded parameter combinations 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: 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 2145213247 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 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: This run will generate roughly 0 Mb of data 62: 62: There were 2 notes 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: 0.6%. 62: The balanceable part of the MD step is 54%, 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: 15 % 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: 19 % 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: 0.005 0.001 378.4 62: (ns/day) (hour/ns) 62: Performance: 1201.950 0.020 62: 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (6 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 -2416675 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 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: This run will generate roughly 0 Mb of data 62: 62: There were 2 notes 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: 0.3%. 62: The balanceable part of the MD step is 60%, 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: 13 % 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: 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: 0.005 0.001 382.5 62: (ns/day) (hour/ns) 62: Performance: 1312.339 0.018 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (6 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 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: 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: 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: 62: Setting gen_seed to 1593749438 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 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: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 5.0%. 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: 2.9%. 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: 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: 0.005 0.001 384.3 62: (ns/day) (hour/ns) 62: Performance: 1116.662 0.021 62: 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: 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: 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: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (5 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 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 -10620930 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 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: 16.6%. 62: The balanceable part of the MD step is 50%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 8.2%. 62: 62: NOTE: 8.2 % 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: 12 % 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: 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: 0.007 0.002 383.6 62: (ns/day) (hour/ns) 62: Performance: 834.248 0.029 62: 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (6 ms) 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (24 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 22 tests from 6 test suites ran. (23841 ms total) 62: [ PASSED ] 21 tests. 62: [ SKIPPED ] 1 test, listed below: 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62/81 Test #62: MdrunTestsTwoRanks ............................. Passed 23.97 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: 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 -37784069 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: 0.007 0.004 197.2 63: (ns/day) (hour/ns) 63: Performance: 518.572 0.046 63: [ OK ] OriresTest.OriresCanRun (114 ms) 63: [----------] 1 test from OriresTest (114 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: 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 -291343 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: 0.018 0.009 198.9 63: (ns/day) (hour/ns) 63: Performance: 506.169 0.047 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 (39851 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: 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 2002763646 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: 0.007 0.004 197.8 63: (ns/day) (hour/ns) 63: Performance: 1274.390 0.019 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 (16486 ms) 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (56337 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 4 tests from 2 test suites ran. (56461 ms total) 63: [ PASSED ] 4 tests. 63/81 Test #63: MdrunSingleRankAlgorithmsTests ................. Passed 56.59 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 0.139 0.1386 8.5877 4.5433 64: [ OK ] NonbondedBenchTest.BasicEndToEndTest (18 ms) 64: [----------] 1 test from NonbondedBenchTest (18 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: 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 = -4.7990997e+01 64: Maximum force = 1.8629692e+02 on atom 13 64: Norm of force = 8.7721836e+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 (150 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: 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 = -5.5862354e+01 64: Maximum force = 4.2726685e+02 on atom 13 64: Norm of force = 1.8452681e+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 (137 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: 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 = 3.1937723e+02 64: Maximum force = 9.9988691e+03 on atom 9 64: Norm of force = 4.6167015e+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 (53 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: 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 = 1.5174414e+02 64: Maximum force = 7.4208760e+03 on atom 9 64: Norm of force = 3.5692977e+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 (52 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: 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 = -1.5698468e+02 64: Maximum force = 4.5702216e+02 on atom 17 64: Norm of force = 1.8327095e+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 (7 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: 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 = 1.06799e+03 on atom 28 64: F-Norm = 4.26914e+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 = -1.6941241e+02 64: Maximum force = 2.1836787e+02 on atom 17 64: Norm of force = 7.9232440e+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 (10 ms) 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (412 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: 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 (6 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: 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 (4 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: 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 (3 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: 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 = 3.1939673e+02 64: Maximum force = 9.9704229e+03 on atom 9 64: Norm of force = 4.6227534e+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 (53 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: 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 = 7.5018237e+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 (53 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: 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 = 5.6111578e+02 64: Maximum force = 1.2685402e+04 on atom 10 64: Norm of force = 6.0643536e+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 (53 ms) 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (175 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: 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: 0.001 0.001 191.3 64: (ns/day) (hour/ns) 64: Performance: 2073.576 0.012 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: 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 0.000 191.4 64: (ns/day) (hour/ns) 64: Performance: 5070.448 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (7 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: 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: 0.002 0.001 194.8 64: (ns/day) (hour/ns) 64: Performance: 1669.990 0.014 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: 0.000 0.000 190.6 64: (ns/day) (hour/ns) 64: Performance: 5784.595 0.004 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (5 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: 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: 0.001 0.001 192.7 64: (ns/day) (hour/ns) 64: Performance: 2316.013 0.010 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: 19 % 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 0.000 192.4 64: (ns/day) (hour/ns) 64: Performance: 4709.934 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (6 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: 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: 0.001 0.001 192.4 64: (ns/day) (hour/ns) 64: Performance: 2156.316 0.011 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: 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: 0.000 0.000 191.3 64: (ns/day) (hour/ns) 64: Performance: 5720.143 0.004 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (5 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: 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: 0.001 0.001 190.7 64: (ns/day) (hour/ns) 64: Performance: 2130.956 0.011 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: 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 0.000 190.9 64: (ns/day) (hour/ns) 64: Performance: 4539.863 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (138 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: 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: 0.007 0.004 198.2 64: (ns/day) (hour/ns) 64: Performance: 399.183 0.060 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: 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 0.000 191.1 64: (ns/day) (hour/ns) 64: Performance: 4210.932 0.006 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (143 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: 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: 0.002 0.001 192.0 64: (ns/day) (hour/ns) 64: Performance: 1805.567 0.013 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: 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: 0.001 0.000 191.7 64: (ns/day) (hour/ns) 64: Performance: 4470.678 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (146 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: 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: 0.003 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 1131.630 0.021 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: 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 0.000 191.7 64: (ns/day) (hour/ns) 64: Performance: 5087.195 0.005 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (141 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: 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: 0.003 0.002 194.6 64: (ns/day) (hour/ns) 64: Performance: 898.963 0.027 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: 18 % 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 0.000 192.8 64: (ns/day) (hour/ns) 64: Performance: 3261.299 0.007 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (11 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: 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: 0.019 0.009 198.9 64: (ns/day) (hour/ns) 64: Performance: 157.798 0.152 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: 30 % 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 0.001 195.3 64: (ns/day) (hour/ns) 64: Performance: 1819.969 0.013 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 196.1 64: (ns/day) (hour/ns) 64: Performance: 751.292 0.032 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: 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: 0.001 0.001 194.7 64: (ns/day) (hour/ns) 64: Performance: 2080.579 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (21 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: 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: 0.003 0.002 195.5 64: (ns/day) (hour/ns) 64: Performance: 832.738 0.029 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: 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 0.001 194.0 64: (ns/day) (hour/ns) 64: Performance: 2407.422 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 ms) 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (668 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: 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: 0.002 0.001 193.0 64: (ns/day) (hour/ns) 64: Performance: 1142.120 0.021 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: 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: 0.004 0.002 195.3 64: (ns/day) (hour/ns) 64: Performance: 774.917 0.031 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: NOTE: 26 % 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 0.002 194.0 64: (ns/day) (hour/ns) 64: Performance: 671.820 0.036 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: 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: 0.001 0.001 193.2 64: (ns/day) (hour/ns) 64: Performance: 1913.822 0.013 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.003 0.002 193.4 64: (ns/day) (hour/ns) 64: Performance: 825.928 0.029 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: 0.001 0.001 193.2 64: (ns/day) (hour/ns) 64: Performance: 2120.686 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (17 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: 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: 0.004 0.002 194.5 64: (ns/day) (hour/ns) 64: Performance: 763.773 0.031 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: 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: 0.002 0.001 192.7 64: (ns/day) (hour/ns) 64: Performance: 1747.686 0.014 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (16 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: 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: 0.003 0.001 193.0 64: (ns/day) (hour/ns) 64: Performance: 1080.048 0.022 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: 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: 0.001 0.001 192.9 64: (ns/day) (hour/ns) 64: Performance: 2533.139 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (13 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: 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: 0.005 0.003 195.6 64: (ns/day) (hour/ns) 64: Performance: 572.280 0.042 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: 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 0.001 188.6 64: (ns/day) (hour/ns) 64: Performance: 2414.972 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (13 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: 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: 0.002 0.001 192.4 64: (ns/day) (hour/ns) 64: Performance: 1201.130 0.020 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: 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: 0.001 0.001 192.1 64: (ns/day) (hour/ns) 64: Performance: 2588.485 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (11 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: 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: 0.002 0.001 192.7 64: (ns/day) (hour/ns) 64: Performance: 1224.527 0.020 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: 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: 0.001 0.001 192.8 64: (ns/day) (hour/ns) 64: Performance: 2757.652 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (11 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: 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: 0.003 0.002 191.8 64: (ns/day) (hour/ns) 64: Performance: 922.659 0.026 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: 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: 0.001 0.001 192.2 64: (ns/day) (hour/ns) 64: Performance: 2330.909 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.002 0.001 192.8 64: (ns/day) (hour/ns) 64: Performance: 1210.095 0.020 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: 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: 0.001 0.001 191.5 64: (ns/day) (hour/ns) 64: Performance: 2543.598 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (11 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: 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: 0.003 0.002 160.0 64: (ns/day) (hour/ns) 64: Performance: 853.268 0.028 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: 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: 0.001 0.001 192.7 64: (ns/day) (hour/ns) 64: Performance: 2265.757 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (14 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: 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: 0.004 0.002 197.2 64: (ns/day) (hour/ns) 64: Performance: 669.921 0.036 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: 0.001 0.001 192.3 64: (ns/day) (hour/ns) 64: Performance: 2164.650 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (13 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: 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: 0.004 0.002 197.1 64: (ns/day) (hour/ns) 64: Performance: 755.716 0.032 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: 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: 0.001 0.001 193.3 64: (ns/day) (hour/ns) 64: Performance: 2374.025 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.006 0.003 197.8 64: (ns/day) (hour/ns) 64: Performance: 523.949 0.046 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: 0.001 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 2322.124 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (13 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: 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: 0.004 0.002 197.2 64: (ns/day) (hour/ns) 64: Performance: 781.504 0.031 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: 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: 0.001 0.001 193.7 64: (ns/day) (hour/ns) 64: Performance: 2303.887 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 197.2 64: (ns/day) (hour/ns) 64: Performance: 779.033 0.031 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: 0.001 0.001 193.6 64: (ns/day) (hour/ns) 64: Performance: 2369.459 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 197.0 64: (ns/day) (hour/ns) 64: Performance: 759.442 0.032 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: 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 0.001 193.5 64: (ns/day) (hour/ns) 64: Performance: 2184.608 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (13 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: 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: 0.003 0.002 196.8 64: (ns/day) (hour/ns) 64: Performance: 889.231 0.027 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: 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: 0.001 0.001 192.1 64: (ns/day) (hour/ns) 64: Performance: 2825.960 0.008 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.005 0.002 197.4 64: (ns/day) (hour/ns) 64: Performance: 612.263 0.039 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: 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: 0.001 0.001 193.0 64: (ns/day) (hour/ns) 64: Performance: 2814.342 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 196.7 64: (ns/day) (hour/ns) 64: Performance: 924.043 0.026 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: 0.001 0.001 192.5 64: (ns/day) (hour/ns) 64: Performance: 2895.016 0.008 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (11 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: 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: 0.003 0.002 196.9 64: (ns/day) (hour/ns) 64: Performance: 869.281 0.028 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: 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: 0.001 0.001 192.0 64: (ns/day) (hour/ns) 64: Performance: 2677.355 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.004 0.002 197.3 64: (ns/day) (hour/ns) 64: Performance: 698.480 0.034 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: 0.001 0.001 192.6 64: (ns/day) (hour/ns) 64: Performance: 2544.648 0.009 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (12 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: 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: 0.003 0.002 194.3 64: (ns/day) (hour/ns) 64: Performance: 902.519 0.027 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: 26 % 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 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 2191.602 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.012 0.006 198.1 64: (ns/day) (hour/ns) 64: Performance: 247.106 0.097 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: 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: 0.001 0.001 193.0 64: (ns/day) (hour/ns) 64: Performance: 2346.893 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (22 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: 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: 0.003 0.001 193.7 64: (ns/day) (hour/ns) 64: Performance: 1036.962 0.023 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: 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: 0.001 0.001 191.8 64: (ns/day) (hour/ns) 64: Performance: 2486.115 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (19 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: 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: 0.005 0.003 196.1 64: (ns/day) (hour/ns) 64: Performance: 540.308 0.044 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: 0.001 0.001 191.8 64: (ns/day) (hour/ns) 64: Performance: 2330.909 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.012 0.006 198.2 64: (ns/day) (hour/ns) 64: Performance: 237.274 0.101 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: 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: 0.001 0.001 192.3 64: (ns/day) (hour/ns) 64: Performance: 2249.213 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (23 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: 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: 0.004 0.002 195.2 64: (ns/day) (hour/ns) 64: Performance: 726.828 0.033 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: 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: 0.001 0.001 192.2 64: (ns/day) (hour/ns) 64: Performance: 2232.908 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (20 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: 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: 0.004 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 816.622 0.029 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: 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: 0.001 0.001 192.5 64: (ns/day) (hour/ns) 64: Performance: 2482.109 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (19 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: 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: 0.003 0.001 194.1 64: (ns/day) (hour/ns) 64: Performance: 981.611 0.024 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: 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: 0.001 0.001 192.7 64: (ns/day) (hour/ns) 64: Performance: 2389.679 0.010 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (18 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: 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: 0.003 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 849.620 0.028 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: 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: 0.001 0.001 193.0 64: (ns/day) (hour/ns) 64: Performance: 2066.620 0.012 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (19 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: 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: 0.004 0.002 195.9 64: (ns/day) (hour/ns) 64: Performance: 651.501 0.037 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: 10 % 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: 1412.009 0.017 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (19 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: 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: 0.008 0.004 196.7 64: (ns/day) (hour/ns) 64: Performance: 377.649 0.064 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: 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: 0.001 0.001 191.9 64: (ns/day) (hour/ns) 64: Performance: 2168.460 0.011 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: 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: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 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 (28 ms) 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (529 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 58 tests from 5 test suites ran. (1819 ms total) 64: [ PASSED ] 58 tests. 64/81 Test #64: MdrunNonIntegratorTests ........................ Passed 1.99 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: 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 (158 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: 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 (146 ms) 65: [----------] 2 tests from Simple/TpiTest (305 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 2 tests from 1 test suite ran. (308 ms total) 65: [ PASSED ] 2 tests. 65/81 Test #65: MdrunTpiTests .................................. Passed 0.43 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 2117548503 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: 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/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: This run will generate roughly 0 Mb of data 66: 66: There were 3 notes 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: 68 % of the run time was spent in domain decomposition, 66: 6 % 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: 5 % 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 0.001 365.9 66: (ns/day) (hour/ns) 66: Performance: 111.060 0.216 66: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (6 ms) 66: [----------] 1 test from DomainDecompositionSpecialCasesTest (6 ms total) 66: 66: [----------] 4 tests from MimicTest 66: [ RUN ] MimicTest.OneQuantumMol 66: Setting the LD random seed to -51531845 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: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 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: 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: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 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: [ OK ] MimicTest.OneQuantumMol (4 ms) 66: [ RUN ] MimicTest.AllQuantumMol 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: 24 % 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: 8 % 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: 0.001 0.000 380.2 66: (ns/day) (hour/ns) 66: Performance: 261.275 0.092 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 Setting the LD random seed to -570601601 66: 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: 66: Generated 10 of the 10 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 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_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: This run will generate roughly 0 Mb of data 66: 66: There were 3 notes 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: 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 (4 ms) 66: Last frame 0 time 0.000 66: 66: NOTE: 22 % of the run time was spent in domain decomposition, 66: 8 % 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 0.001 322.8 66: (ns/day) (hour/ns) 66: Performance: 147.312 0.163 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 [ RUN ] MimicTest.TwoQuantumMol 66: Setting the LD random seed to -16801 66: 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: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generating 1-4 interactions: fudge = 0.5 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: 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: 23 % 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: 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: 0.001 0.000 370.7 66: (ns/day) (hour/ns) 66: Performance: 255.653 0.094 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 (4 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 -13107201 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: 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: 26 % 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 0.000 383.3 66: (ns/day) (hour/ns) 66: Performance: 200.880 0.119 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 (9 ms) 66: [----------] 4 tests from MimicTest (24 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: 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 = -4.7990952e+01 66: Maximum force = 1.8629709e+02 on atom 13 66: Norm of force = 8.7721970e+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 (148 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: This run will generate roughly 0 Mb of data 66: 66: There were 3 notes 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 = -5.5862228e+01 66: Maximum force = 4.2727219e+02 on atom 13 66: Norm of force = 1.8452919e+02 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (139 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 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 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: 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: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (54 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 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 = 3.1937720e+02 66: Maximum force = 9.9988691e+03 on atom 9 66: Norm of force = 4.6167015e+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 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: Generating 1-4 interactions: fudge = 1 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: 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: 66: This run will generate roughly 0 Mb of data 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: 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 = 1.5174358e+02 66: Maximum force = 7.4208833e+03 on atom 9 66: Norm of force = 3.5692986e+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 (52 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: 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: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 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: 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: 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: 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: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (9 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 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 = -1.5698456e+02 66: Maximum force = 4.5702222e+02 on atom 17 66: Norm of force = 1.8327095e+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 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: 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: 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/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: There were 5 notes 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 = 1.06799e+03 on atom 28 66: F-Norm = 4.26914e+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 = -1.6941235e+02 66: Maximum force = 2.1838167e+02 on atom 17 66: Norm of force = 7.9235200e+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 (10 ms) 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (415 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: 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 (4 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: Number of degrees of freedom in T-Coupling group System is 33.00 66: This run will generate roughly 0 Mb of data 66: 66: There were 2 notes 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: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (4 ms) 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/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 [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 66: Generated 1 of the 1 non-bonded parameter combinations 66: 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: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: This run will generate roughly 0 Mb of data 66: 66: There were 2 notes 66: 66: There was 1 warning 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 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: Generating 1-4 interactions: fudge = 1 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: 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: 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: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (52 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/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 = 3.1939664e+02 66: Maximum force = 9.9704229e+03 on atom 9 66: Norm of force = 4.6227537e+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 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: 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: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (52 ms) 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 = 1.5625764e+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 [ 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 (49 ms) 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (166 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 17 tests from 4 test suites ran. (653 ms total) 66: [ PASSED ] 17 tests. 66/81 Test #66: MdrunMpiTests .................................. Passed 0.80 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_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: 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: Setting the LD random seed to -1161830473 67: Setting the LD random seed to -1310859269 67: 67: 67: Generated 3 of the 3 non-bonded 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: Setting gen_seed to -1076101266 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: 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: 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: 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: 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: 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: 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: 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: 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: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -1342439437 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 -152224385 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 -806486089 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 1539309533 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 -1327547205 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: 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: 67: Writing final coordinates. 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: 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: 67: Writing final coordinates. 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: 67: Writing final coordinates. 67: [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (9 ms) 67: [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 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: 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: 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: 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: Setting the LD random seed to -185434245 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 -1317076996 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 -508151841 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 -479496225 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 -16781333 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 -370415633 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: [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (4 ms) 67: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 67: Setting the LD random seed to -37766561 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 2138565093 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 -404818347 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 -1476666956 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 -86675783 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 -9470721 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: 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 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: 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: 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: 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: 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: 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: 1 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: Writing final coordinates. 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: 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: Note: The number of steps is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Writing final coordinates. 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: 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: 3 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: Writing final coordinates. 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: 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: 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: 16 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (5 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: 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_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_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: 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: 1 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: Writing final coordinates. 67: 67: NOTE: 18 % of the run time was spent in domain decomposition, 67: 2 % 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: 24 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 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: 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_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: 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: 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: 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: 22 % of the run time was spent in domain decomposition, 67: 11 % 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: Setting the LD random seed to -814391299 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 -335994981 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 -67379393 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 1341910391 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: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (4 ms) 67: [----------] 4 tests from InNvt/MultiSimTest (25 ms total) 67: 67: [----------] 2 tests from InNvt/MultiSimTerminationTest 67: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 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: 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_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: 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: 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: 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: 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_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: 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: 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: 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: 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_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: 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: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 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: 100 steps, 0.1 ps. 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: 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_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: 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: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 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: 100 steps, 0.1 ps. 67: Setting the LD random seed to -145756164 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 -83906625 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 -721821709 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 1979711485 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 -540196943 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 -27871682 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 -2014349316 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 -273203205 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: Step 10: Run time exceeded 0.000 hours, will terminate the run within 2 steps 67: 67: NOTE: 22 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 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: 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 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: 13 steps, 0.0 ps (continuing from step 11, 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: Step 14: Run time exceeded 0.000 hours, will terminate the run within 2 steps 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: 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: 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 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: 17 steps, 0.0 ps (continuing from step 15, 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: Step 12: Run time exceeded 0.000 hours, will terminate the run within 2 steps 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: 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 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: 15 steps, 0.0 ps (continuing from step 13, 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: Step 8: Run time exceeded 0.000 hours, will terminate the run within 2 steps 67: 67: NOTE: 23 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 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: 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: 11 steps, 0.0 ps (continuing from step 9, 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 (7 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: 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_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: 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 6: 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: 7.8%. 67: The balanceable part of the MD step is 17%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 1.3%. 67: 67: 67: NOTE: 27 % of the run time was spent in domain decomposition, 67: 6 % 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: 23 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 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: 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_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: 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 6: 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: 9.3%. 67: The balanceable part of the MD step is 17%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 1.6%. 67: 67: 67: NOTE: 26 % 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: 24 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: Setting the LD random seed to 2139029115 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 2145383870 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 -556282045 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 -8400899 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: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (7 ms) 67: [----------] 2 tests from InNvt/MultiSimTerminationTest (14 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 6 tests from 2 test suites ran. (67 ms total) 67: [ PASSED ] 6 tests. 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: 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 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: 9 steps, 0.0 ps (continuing from step 7, 0.0 ps). 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: 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: 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: 9 steps, 0.0 ps (continuing from step 7, 0.0 ps). 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 67/81 Test #67: MdrunMultiSimTests ............................. Passed 0.22 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: 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: 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: 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_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: Setting the LD random seed to -1073776705 68: Setting the LD random seed to 2109731182 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 -1090662494 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: Setting the LD random seed to 2077458110 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 -673588626 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: 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 -24723 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: 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: 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/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: 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/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: There were 2 notes 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: Setting the LD random seed to 1273363320 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: 68: Setting gen_seed to -361042945 68: 68: Velocities were taken from a Maxwell distribution at 268 K 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: This run will generate roughly 0 Mb of data 68: 68: There were 2 notes 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: 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: 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: 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 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: 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: 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: 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: 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 (7 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_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_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_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: Setting the LD random seed to 2080374748 68: Setting the LD random seed to -1078198411 68: Setting the LD random seed to -608371041 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: Generating 1-4 interactions: fudge = 0.5 68: Generating 1-4 interactions: fudge = 0.5 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: Generating 1-4 interactions: fudge = 0.5 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 -539372821 68: 68: Velocities were taken from a Maxwell distribution at 268 K 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -542778126 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: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to 1824517597 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_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_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 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: 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/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_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: Setting the LD random seed to -682692649 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 -156532741 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: 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: 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_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_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_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 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 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: 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: 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: 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/1 (5 ms) 68: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 68: Setting the LD random seed to -168198345 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 -4768713 68: 68: Velocities were taken from a Maxwell distribution at 278 K 68: Setting the LD random seed to -287446093 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 -537068107 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_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: 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/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: Generating 1-4 interactions: fudge = 0.5 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: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps 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: 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: This run will generate roughly 0 Mb of data 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: 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: There were 2 notes 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: 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: 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: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 1.9%. 68: The balanceable part of the MD step is 24%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.4%. 68: 68: 68: NOTE: 14 % of the run time was spent in domain decomposition, 68: 4 % 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: 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: 20.5%. 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: 6.1%. 68: 68: NOTE: 6.1 % 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: NOTE: 14 % 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: 29 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (5 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_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: 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: 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: 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: 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: 1.4%. 68: The balanceable part of the MD step is 12%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.2%. 68: 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: 23 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 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 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: 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: 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: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 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: 39.9%. 68: The balanceable part of the MD step is 18%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 7.2%. 68: 68: NOTE: 7.2 % 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: NOTE: 15 % 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: 22 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: Setting the LD random seed to -18874499 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 1043984805 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: Setting the LD random seed to 2080240359 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 -674234459 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: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (4 ms) 68: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (23 ms total) 68: 68: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 68: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 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_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: 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: 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: 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: 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: 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: 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: 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: Setting the LD random seed to -142606357 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 -6389770 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: Setting the LD random seed to 1509020476 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 2003957112 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: Setting the LD random seed to -1242038579 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 -1082529547 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: Setting the LD random seed to -341519908 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 -100767921 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: 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 4: Run time exceeded 0.000 hours, will terminate the run within 400 steps 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 4: Run time exceeded 0.000 hours, will terminate the run within 400 steps 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 4: Run time exceeded 0.000 hours, will terminate the run within 400 steps 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 4: Run time exceeded 0.000 hours, will terminate the run within 400 steps 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: NOTE: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 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 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: 68: Writing final coordinates. 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: 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: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 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: 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: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 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: 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: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 68: 68: Writing final coordinates. 68: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (14 ms) 68: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (15 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 5 tests from 2 test suites ran. (64 ms total) 68: [ PASSED ] 5 tests. 68/81 Test #68: MdrunMultiSimReplexTests ....................... Passed 0.21 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: 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_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_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: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s 69: Generating 1-4 interactions: fudge = 0.5 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: 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: 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: 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 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: 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: 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: Number of degrees of freedom in T-Coupling group System is 27.00 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_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: 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_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: This run will generate roughly 0 Mb of data 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: 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_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: 69: There were 2 notes 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: 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: 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_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: 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_0/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: 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: 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: 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: 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: 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: 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: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (179 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generated 330891 of the 330891 non-bonded parameter combinations 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: 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 288 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: 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 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_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: There were 2 notes 69: 69: There was 1 warning 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/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: 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: 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_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: 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: 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: 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_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_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: 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: 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 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: 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_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: 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: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (168 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s 69: Generating 1-4 interactions: fudge = 0.5 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: 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: 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 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 288 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: 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 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: 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_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: 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: 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_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: 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: 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_2/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: 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_1/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: 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: 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: 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_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: 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_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: 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: 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_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: 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: 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: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (163 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s 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: 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: 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: Velocities were taken from a Maxwell distribution at 278 K 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 288 K 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 268 K 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_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: 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: 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: 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_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: 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: 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: 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_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: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 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: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 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: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 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: 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 (157 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 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/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: 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_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: 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_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: 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: 0.5%. 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: 0.3%. 69: 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: 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: 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: 1.0%. 69: The balanceable part of the MD step is 53%, 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: 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: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (146 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s 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: 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: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 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/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: 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: 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: 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: 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: 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: 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: 0.6%. 69: The balanceable part of the MD step is 53%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.3%. 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: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 1.0%. 69: The balanceable part of the MD step is 55%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.6%. 69: 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 (144 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: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 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: 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 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: This run will generate roughly 0 Mb of data 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: 69: There were 3 notes 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: 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: 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: 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: 0.2%. 69: The balanceable part of the MD step is 23%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.1%. 69: 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: 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: 3.6%. 69: The balanceable part of the MD step is 23%, 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 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: 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: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (145 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s 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: 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 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: 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: 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_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: 0.9%. 69: The balanceable part of the MD step is 56%, 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: 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: 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: 0.4%. 69: The balanceable part of the MD step is 55%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.2%. 69: 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: 7 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (144 ms) 69: [----------] 8 tests from LF/ReplicaExchangeTest (1253 ms total) 69: 69: [----------] 2 tests from VV/ReplicaExchangeTest 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: [ 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_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_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_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: 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: 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: 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: 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: 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: 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_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: 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: 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: 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: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 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/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: There were 2 notes 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/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: There were 2 notes 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: There were 2 notes 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: 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: 69: Writing final coordinates. 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: 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: 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: 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: 69: Writing final coordinates. 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: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 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 (159 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: 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: 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_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: 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: 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: 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 40%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.6%. 69: 69: 69: NOTE: 11 % 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: 8 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 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: 0.9%. 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: 0.3%. 69: 69: 69: NOTE: 11 % 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: 8 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (146 ms) 69: [----------] 2 tests from VV/ReplicaExchangeTest (306 ms total) 69: 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: [----------] Global test environment tear-down 69: [==========] 10 tests from 2 test suites ran. (1586 ms total) 69: [ PASSED ] 10 tests. 69/81 Test #69: MdrunMultiSimReplexEquivalenceTests ............ Passed 1.74 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 -1078567505 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: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 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: 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: 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: Setting the LD random seed to -17106185 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 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: 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: 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: 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: 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: 0.025 0.012 199.4 70: (ns/day) (hour/ns) 70: Performance: 146.386 0.164 70: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (9728 ms) 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 [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 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: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (15 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: 70: Core t (s) Wall t (s) (%) 70: Time: 0.024 0.012 199.3 70: (ns/day) (hour/ns) 70: Performance: 153.896 0.156 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 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: 0.004 0.002 195.0 70: (ns/day) (hour/ns) 70: Performance: 37.776 0.635 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: [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (29996 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: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ 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: 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: 0.023 0.012 199.3 70: (ns/day) (hour/ns) 70: Performance: 156.410 0.153 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 (15 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 (39756 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 19 tests from 1 test suite ran. (39769 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 39.90 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 -1612843467 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: The largest distance between excluded atoms is 0.190 nm 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: 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: 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: This run will generate roughly 0 Mb of data 71: 71: There were 2 notes 71: Setting the LD random seed to -1286131777 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: 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: The largest distance between excluded atoms is 0.190 nm 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: 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: 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: This run will generate roughly 0 Mb of data 71: 71: There were 3 notes 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 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: 0.9%. 71: The balanceable part of the MD step is 15%, 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: 8 % 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: 0.042 0.011 398.1 71: (ns/day) (hour/ns) 71: Performance: 172.234 0.139 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 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 (9718 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 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: 1.1%. 71: The balanceable part of the MD step is 15%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.2%. 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.039 0.010 398.1 71: (ns/day) (hour/ns) 71: Performance: 186.359 0.129 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 (13 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: 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: 0.008 0.002 380.1 71: (ns/day) (hour/ns) 71: Performance: 43.706 0.549 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 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (30610 ms) 71: [ RUN ] 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_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: 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: 10.282 2.570 400.0 71: (ns/day) (hour/ns) 71: Performance: 0.706 34.001 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 (5132 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 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: 0.046 0.011 398.1 71: (ns/day) (hour/ns) 71: Performance: 158.028 0.152 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 (14 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: 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: 39.103 9.776 400.0 71: (ns/day) (hour/ns) 71: Performance: 0.009 2715.533 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 (19552 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: 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: 1.3%. 71: The balanceable part of the MD step is 16%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.2%. 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.038 0.009 398.1 71: (ns/day) (hour/ns) 71: Performance: 191.769 0.125 71: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (12 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: 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 [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [----------] 19 tests from ReproducesEnergies/PmeTest (65056 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 19 tests from 1 test suite ran. (65072 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 65.22 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: 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: 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: There were 3 notes 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 98.1 72: (ns/day) (hour/ns) 72: Performance: 814.355 0.029 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 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: 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: There were 3 notes 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: 0.001 0.001 95.7 72: (ns/day) (hour/ns) 72: Performance: 2338.874 0.010 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: 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 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: 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 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: 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: 0.001 0.001 95.1 72: (ns/day) (hour/ns) 72: Performance: 2762.598 0.009 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 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: 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: 0.001 0.001 95.3 72: (ns/day) (hour/ns) 72: Performance: 2557.324 0.009 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: 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: 0.001 0.001 95.2 72: (ns/day) (hour/ns) 72: Performance: 2663.465 0.009 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: Generated 1 of the 1 non-bonded parameter combinations 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: 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: 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: 0.001 0.001 95.4 72: (ns/day) (hour/ns) 72: Performance: 2483.109 0.010 72: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (27 ms) 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: [----------] 1 test from BasicPropagators/PeriodicActionsTest (27 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 1 test from 1 test suite ran. (36 ms total) 72: [ PASSED ] 1 test. 72/81 Test #72: MdrunMpiCoordinationBasicTestsOneRank .......... Passed 0.18 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: 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: 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: 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: 6.7%. 73: The balanceable part of the MD step is 57%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 3.9%. 73: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 73: 73: 73: NOTE: 37 % 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 0.003 195.8 73: (ns/day) (hour/ns) 73: Performance: 531.957 0.045 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: 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: 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: 2.8%. 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: 1.7%. 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: 0.003 0.001 188.2 73: (ns/day) (hour/ns) 73: Performance: 1099.713 0.022 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 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 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 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 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 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 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 0.004 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 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 6 time 0.006 Reading energy frame 6 time 0.006 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 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/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: 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 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: 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 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: 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: 2.2%. 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: 1.3%. 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: 0.002 0.001 189.4 73: (ns/day) (hour/ns) 73: Performance: 1706.536 0.014 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: 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/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: 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 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 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 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 13 time 0.013 Reading energy frame 6 time 0.006 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 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: 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: 73: Excluding 1 bonded neighbours molecule type 'Argon' 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: 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: 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: 2.4%. 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: 1.4%. 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: 0.002 0.001 184.2 73: (ns/day) (hour/ns) 73: Performance: 1532.105 0.016 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: 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: 2.3%. 73: The balanceable part of the MD step is 55%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 1.3%. 73: 73: 73: NOTE: 36 % 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: 0.002 0.001 189.1 73: (ns/day) (hour/ns) 73: Performance: 1456.233 0.016 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: 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: 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: 1.3%. 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: 36 % 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: 0.002 0.001 189.5 73: (ns/day) (hour/ns) 73: Performance: 1580.855 0.015 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 (38 ms) 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest (38 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (49 ms total) 73: [ PASSED ] 1 test. 73/81 Test #73: MdrunMpiCoordinationBasicTestsTwoRanks ......... Passed 0.19 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: 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: There were 3 notes 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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_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 98.1 74: (ns/day) (hour/ns) 74: Performance: 750.651 0.032 74: Generated 1 of the 1 non-bonded parameter combinations 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_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: There were 3 notes 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 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1804.509 0.013 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: 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: 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: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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 0.001 94.7 74: (ns/day) (hour/ns) 74: Performance: 2460.301 0.010 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2334.442 0.010 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 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: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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 0.001 94.4 74: (ns/day) (hour/ns) 74: Performance: 2385.054 0.010 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: 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: 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2420.666 0.010 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (30 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1654.295 0.015 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: 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: 0.001 0.001 95.6 74: (ns/day) (hour/ns) 74: Performance: 2060.399 0.012 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 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: 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2655.428 0.009 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 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_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: 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: 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: 0.001 0.001 94.5 74: (ns/day) (hour/ns) 74: Performance: 2438.873 0.010 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: 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2440.806 0.010 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: 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: 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: 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (27 ms) 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 95.4 74: (ns/day) (hour/ns) 74: Performance: 2297.872 0.010 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: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 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_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: 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: 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 96.5 74: (ns/day) (hour/ns) 74: Performance: 1770.794 0.014 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_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: 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: 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 95.8 74: (ns/day) (hour/ns) 74: Performance: 2178.428 0.011 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: 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 95.3 74: (ns/day) (hour/ns) 74: Performance: 2289.332 0.010 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: 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 94.9 74: (ns/day) (hour/ns) 74: Performance: 2550.970 0.009 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: 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 94.4 74: (ns/day) (hour/ns) 74: Performance: 2341.541 0.010 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: 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: 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: 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 95.3 74: (ns/day) (hour/ns) 74: Performance: 2425.431 0.010 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (27 ms) 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: [ 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: 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 2 notes 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 96.3 74: (ns/day) (hour/ns) 74: Performance: 2108.348 0.011 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_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: 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: 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 95.6 74: (ns/day) (hour/ns) 74: Performance: 2443.710 0.010 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: 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: 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: 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 94.2 74: (ns/day) (hour/ns) 74: Performance: 2713.918 0.009 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 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: 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: 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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: 0.001 0.001 94.5 74: (ns/day) (hour/ns) 74: Performance: 2521.733 0.010 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Note that 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: 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 94.9 74: (ns/day) (hour/ns) 74: Performance: 2735.610 0.009 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: 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: 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: 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 95.2 74: (ns/day) (hour/ns) 74: Performance: 2710.336 0.009 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (24 ms) 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: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 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_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: 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: 74: There was 1 warning 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: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 1889.173 0.013 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: 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: 0.001 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2236.962 0.011 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: 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: 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: 0.001 0.001 94.3 74: (ns/day) (hour/ns) 74: Performance: 2570.127 0.009 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: 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: There were 2 notes 74: 74: There was 1 warning 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_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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2354.067 0.010 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2705.575 0.009 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: 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: 74: There was 1 warning 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2324.752 0.010 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 (25 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1592.296 0.015 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: 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: 0.001 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 2209.682 0.011 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 0.000 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2804.094 0.009 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 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: 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: 0.001 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2485.112 0.010 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2649.718 0.009 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: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 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: 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: 0.001 0.001 94.0 74: (ns/day) (hour/ns) 74: Performance: 2418.765 0.010 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (24 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 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_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: 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: 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: 0.001 0.001 96.0 74: (ns/day) (hour/ns) 74: Performance: 2084.803 0.012 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: 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2422.569 0.010 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: 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: 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: 0.001 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2539.404 0.009 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: 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2592.842 0.009 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: 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2542.548 0.009 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: 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_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: 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2556.263 0.009 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 (24 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: 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: 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 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 1970.129 0.012 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: 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 3 notes 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 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2702.015 0.009 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: 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: 0.000 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2846.855 0.008 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 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: 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: 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: 0.000 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2825.960 0.008 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: 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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_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 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2791.388 0.009 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: 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: 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 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2690.216 0.009 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 (24 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: 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: There were 3 notes 74: 74: There was 1 warning 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: 74: Note 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 2031.188 0.012 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: 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: 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: 0.001 0.001 95.6 74: (ns/day) (hour/ns) 74: Performance: 2216.041 0.011 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 0.000 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2786.338 0.009 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: 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: 0.000 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2858.744 0.008 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2658.867 0.009 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: 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: 74: There were 3 notes 74: 74: There was 1 warning 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: 0.000 0.001 94.8 74: (ns/day) (hour/ns) 74: Performance: 2873.411 0.008 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: This run will generate roughly 0 Mb of data 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 (24 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: 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 3 notes 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: 0.001 0.001 95.8 74: (ns/day) (hour/ns) 74: Performance: 2193.163 0.011 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2663.465 0.009 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 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: 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 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: 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: 0.001 0.001 95.2 74: (ns/day) (hour/ns) 74: Performance: 2719.909 0.009 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: 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: 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: 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: 0.001 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2435.017 0.010 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: 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: 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 3 notes 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: 0.001 0.001 93.6 74: (ns/day) (hour/ns) 74: Performance: 2535.224 0.009 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 2637.240 0.009 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (25 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 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: 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: 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: 0.001 0.001 95.4 74: (ns/day) (hour/ns) 74: Performance: 1919.188 0.013 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: 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: Generated 1 of the 1 non-bonded parameter combinations 74: 74: There were 3 notes 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: 0.001 0.001 95.4 74: (ns/day) (hour/ns) 74: Performance: 2448.567 0.010 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 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: 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 3 notes 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: 0.000 0.001 94.1 74: (ns/day) (hour/ns) 74: Performance: 2777.545 0.009 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: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 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: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 2757.652 0.009 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: 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: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 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: 0.001 0.001 92.2 74: (ns/day) (hour/ns) 74: Performance: 2500.241 0.010 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: 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 0.001 0.001 94.0 74: (ns/day) (hour/ns) 74: Performance: 2371.283 0.010 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (25 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: 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Note that 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: 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 96.9 74: (ns/day) (hour/ns) 74: Performance: 1811.939 0.013 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_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: 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: 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 96.2 74: (ns/day) (hour/ns) 74: Performance: 2642.897 0.009 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 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_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: 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_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: 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: 0.000 0.000 95.8 74: (ns/day) (hour/ns) 74: Performance: 3091.116 0.008 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: Generated 1 of the 1 non-bonded parameter combinations 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: 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 96.3 74: (ns/day) (hour/ns) 74: Performance: 2200.998 0.011 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: 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: 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_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: 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 94.0 74: (ns/day) (hour/ns) 74: Performance: 2523.799 0.010 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 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: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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 96.5 74: (ns/day) (hour/ns) 74: Performance: 1956.987 0.012 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 (26 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: 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: 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: Generated 1 of the 1 non-bonded parameter combinations 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1707.955 0.014 74: Generated 1 of the 1 non-bonded parameter combinations 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_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: 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: 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 96.3 74: (ns/day) (hour/ns) 74: Performance: 2309.934 0.010 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: 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: 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 95.6 74: (ns/day) (hour/ns) 74: Performance: 2716.311 0.009 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: 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 95.7 74: (ns/day) (hour/ns) 74: Performance: 2648.579 0.009 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: 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: 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 95.8 74: (ns/day) (hour/ns) 74: Performance: 2387.827 0.010 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: 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: 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 95.8 74: (ns/day) (hour/ns) 74: Performance: 2459.319 0.010 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 (25 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: 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1878.803 0.013 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: 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: 0.001 0.001 96.3 74: (ns/day) (hour/ns) 74: Performance: 2291.888 0.010 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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: 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: 0.001 0.001 94.9 74: (ns/day) (hour/ns) 74: Performance: 2559.449 0.009 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: There were 2 notes 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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: 0.001 0.001 95.8 74: (ns/day) (hour/ns) 74: Performance: 2330.909 0.010 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: 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: 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: 0.001 0.001 95.9 74: (ns/day) (hour/ns) 74: Performance: 2339.762 0.010 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: 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: 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: 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: 0.001 0.001 95.1 74: (ns/day) (hour/ns) 74: Performance: 2418.765 0.010 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 (25 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 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: 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: 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: 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: 0.001 0.001 98.0 74: (ns/day) (hour/ns) 74: Performance: 1567.980 0.015 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: 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1751.164 0.014 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: 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_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: 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: 0.001 0.001 97.6 74: (ns/day) (hour/ns) 74: Performance: 1735.379 0.014 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: 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: 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_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: 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: 0.001 0.001 97.6 74: (ns/day) (hour/ns) 74: Performance: 1919.188 0.013 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: 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_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: 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: 0.001 0.001 97.6 74: (ns/day) (hour/ns) 74: Performance: 1894.402 0.013 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: 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_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: 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: 0.001 0.001 97.5 74: (ns/day) (hour/ns) 74: Performance: 1855.042 0.013 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 (26 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: Generated 1 of the 1 non-bonded parameter combinations 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: 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: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 97.9 74: (ns/day) (hour/ns) 74: Performance: 1432.030 0.017 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: 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1860.083 0.013 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 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: 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: 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: 0.001 0.001 97.6 74: (ns/day) (hour/ns) 74: Performance: 1881.672 0.013 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 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: Generated 1 of the 1 non-bonded parameter combinations 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: 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: 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: 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: 0.001 0.001 97.4 74: (ns/day) (hour/ns) 74: Performance: 1847.254 0.013 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: 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: 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: 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: 0.001 0.001 97.6 74: (ns/day) (hour/ns) 74: Performance: 1686.910 0.014 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: 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: 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: 0.001 0.001 97.5 74: (ns/day) (hour/ns) 74: Performance: 1926.390 0.012 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (27 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1759.164 0.014 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: 74: There were 2 notes 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: This run will generate roughly 0 Mb of data 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1767.239 0.014 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: 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: 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: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 2299.587 0.010 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: 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 2099.010 0.011 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: 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: 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: 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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1941.568 0.012 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: 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: 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1945.860 0.012 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 (25 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: 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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1697.133 0.014 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_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: 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 2 notes 74: 74: There was 1 warning 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1772.833 0.014 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 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 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 (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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: There were 2 notes 74: 74: There was 1 warning 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: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This 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: 1575.197 0.015 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 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_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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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: 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: 0.001 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1897.903 0.013 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: Generated 1 of the 1 non-bonded parameter combinations 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: 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: 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_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: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 1864.586 0.013 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: 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: 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (26 ms) 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 97.0 74: (ns/day) (hour/ns) 74: Performance: 1665.475 0.014 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: [ 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: Generated 1 of the 1 non-bonded parameter combinations 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: 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: 0.001 0.001 97.1 74: (ns/day) (hour/ns) 74: Performance: 1557.278 0.015 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_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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1857.279 0.013 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 Generated 1 of the 1 non-bonded parameter combinations 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: 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: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1832.419 0.013 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 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_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: 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: 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: 0.001 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1694.333 0.014 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1691.077 0.014 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: 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_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: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 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: 0.001 0.001 96.7 74: (ns/day) (hour/ns) 74: Performance: 1631.081 0.015 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (26 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 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: 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: 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: 0.001 0.001 97.8 74: (ns/day) (hour/ns) 74: Performance: 1204.417 0.020 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: 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: 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: 0.001 0.001 97.3 74: (ns/day) (hour/ns) 74: Performance: 1225.257 0.020 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: 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: 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: 0.001 0.001 96.8 74: (ns/day) (hour/ns) 74: Performance: 1465.761 0.016 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: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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_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: 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: 0.001 0.001 96.9 74: (ns/day) (hour/ns) 74: Performance: 1612.299 0.015 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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_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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1586.555 0.015 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: 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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_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: 0.001 0.001 97.3 74: (ns/day) (hour/ns) 74: Performance: 1500.754 0.016 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 (27 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: 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: 0.002 0.002 97.3 74: (ns/day) (hour/ns) 74: Performance: 930.041 0.026 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: 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: 0.001 0.001 97.3 74: (ns/day) (hour/ns) 74: Performance: 1178.835 0.020 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 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: 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: 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: 0.001 0.001 97.5 74: (ns/day) (hour/ns) 74: Performance: 1164.133 0.021 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: 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: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 0.001 0.002 87.2 74: (ns/day) (hour/ns) 74: Performance: 960.043 0.025 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: 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: 0.001 0.001 97.5 74: (ns/day) (hour/ns) 74: Performance: 1049.505 0.023 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that 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: 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: 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: 0.001 0.001 97.4 74: (ns/day) (hour/ns) 74: Performance: 1097.167 0.022 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (30 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 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_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: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 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: 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: 0.001 0.001 97.4 74: (ns/day) (hour/ns) 74: Performance: 1347.167 0.018 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: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note 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: 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: 0.001 0.001 97.3 74: (ns/day) (hour/ns) 74: Performance: 1434.698 0.017 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 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: 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: 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: 0.001 0.001 97.1 74: (ns/day) (hour/ns) 74: Performance: 1681.385 0.014 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 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1524.522 0.016 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: There were 2 notes 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_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: 0.001 0.001 97.1 74: (ns/day) (hour/ns) 74: Performance: 1341.301 0.018 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: 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: 0.001 0.001 97.2 74: (ns/day) (hour/ns) 74: Performance: 1475.238 0.016 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (26 ms) 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (579 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 22 tests from 1 test suite ran. (590 ms total) 74: [ PASSED ] 22 tests. 74/81 Test #74: MdrunMpiCoordinationCouplingTestsOneRank ....... Passed 0.75 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: 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: 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: 1.7%. 75: The balanceable part of the MD step is 48%, 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: 38 % of the run time was 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: 712.537 0.034 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: 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: 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: 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 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 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 59%, 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: 0.002 0.001 190.3 75: (ns/day) (hour/ns) 75: Performance: 1471.538 0.016 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 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 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 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 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_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: 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: 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: Reading energy frame 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 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 3.3%. 75: The balanceable part of the MD step is 47%, 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: 11 % of the run time was spent in domain decomposition, 75: 4 % 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: 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: 0.001 0.001 189.1 75: (ns/day) (hour/ns) 75: Performance: 2074.623 0.012 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 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 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.012 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 3 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 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 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 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 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: 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: 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: 3.6%. 75: The balanceable part of the MD step is 48%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.7%. 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: 0.001 0.001 189.6 75: (ns/day) (hour/ns) 75: Performance: 1870.815 0.013 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_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: 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: 3.5%. 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: 1.6%. 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: 0.002 0.001 192.0 75: (ns/day) (hour/ns) 75: Performance: 1457.439 0.016 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_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: 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: 1.3%. 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: 0.7%. 75: 75: 75: NOTE: 12 % 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: 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: 0.002 0.001 190.3 75: (ns/day) (hour/ns) 75: Performance: 1623.987 0.015 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 (35 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 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: 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: 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: 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: 3.5%. 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: 2.0%. 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: 0.002 0.001 191.3 75: (ns/day) (hour/ns) 75: Performance: 1292.342 0.019 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: 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: 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: 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: 2.1%. 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: 1.2%. 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: 0.002 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1533.821 0.016 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 0.001 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_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 0.001 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_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: 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 enseGenerated 1 of the 1 non-bonded parameter combinations 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: mble 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: 9.9%. 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: 4.8%. 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: 0.002 0.001 189.3 75: (ns/day) (hour/ns) 75: Performance: 1585.738 0.015 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_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 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 11 time 0.011 Reading energy frame 12 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 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 Last energy frame read 4 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 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: 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_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: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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 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: 1.5%. 75: The balanceable part of the MD step is 50%, 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: 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: 0.002 0.001 189.1 75: (ns/day) (hour/ns) 75: Performance: 1598.908 0.015 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: 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_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: 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: 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: 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: 5.1%. 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: 2.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 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: 0.002 0.001 189.6 75: (ns/day) (hour/ns) 75: Performance: 1633.243 0.015 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: 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_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: 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: 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: 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (31 ms) 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: 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: 3.4%. 75: The balanceable part of the MD step is 50%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.7%. 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: 0.002 0.001 191.9 75: (ns/day) (hour/ns) 75: Performance: 1334.328 0.018 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: [ 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: 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: 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: 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: 2.1%. 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: 1.2%. 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: 0.002 0.001 191.3 75: (ns/day) (hour/ns) 75: Performance: 1235.950 0.019 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: 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: 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: 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: 3.3%. 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: 1.9%. 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: 0.002 0.001 189.5 75: (ns/day) (hour/ns) 75: Performance: 1485.196 0.016 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 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 Generated 1 of the 1 non-bonded parameter combinations 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: 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: 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: 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: 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: 7.4%. 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: 3.6%. 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: 0.002 0.001 189.5 75: (ns/day) (hour/ns) 75: Performance: 1565.191 0.015 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 Reading energy frame 1 time 0.001 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_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: 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 Reading energy frame 1 time 0.001 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: 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: 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: 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: There were 3 notes 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: 3.4%. 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: 1.7%. 75: 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: 0.002 0.001 190.3 75: (ns/day) (hour/ns) 75: Performance: 1589.626 0.015 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: 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: 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_2_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: 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: 5.4%. 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: 2.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 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: 0.002 0.001 189.0 75: (ns/day) (hour/ns) 75: Performance: 1624.843 0.015 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_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: 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: 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: 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: There were 3 notes 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: 5.6%. 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: 3.0%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 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: 0.002 0.001 188.9 75: (ns/day) (hour/ns) 75: Performance: 1594.357 0.015 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (32 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: 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: 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: 0.002 0.001 190.9 75: (ns/day) (hour/ns) 75: Performance: 1624.201 0.015 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: 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: Generated 1 of the 1 non-bonded parameter combinations 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 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: 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: 0.002 0.001 189.5 75: (ns/day) (hour/ns) 75: Performance: 1557.278 0.015 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 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_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: 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: 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 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: 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: 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: 0.001 0.001 187.6 75: (ns/day) (hour/ns) 75: Performance: 1991.142 0.012 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 0.004 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_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: 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: 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: 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: 0.002 0.001 186.9 75: (ns/day) (hour/ns) 75: Performance: 1825.902 0.013 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_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: 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: Generated 1 of the 1 non-bonded parameter combinations 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: 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: 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: 0.002 0.001 187.9 75: (ns/day) (hour/ns) 75: Performance: 1603.904 0.015 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: 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: 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: 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 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: 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: 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: 0.001 0.001 186.6 75: (ns/day) (hour/ns) 75: Performance: 1830.786 0.013 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 (32 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: 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: 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: Generated 1 of the 1 non-bonded parameter combinations 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: 0.002 0.001 190.0 75: (ns/day) (hour/ns) 75: Performance: 1345.402 0.018 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: 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: 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: Generated 1 of the 1 non-bonded parameter combinations 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 0.001 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: 0.002 0.001 187.4 75: (ns/day) (hour/ns) 75: Performance: 1629.571 0.015 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 0.001 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_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: 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: 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: There were 2 notes 75: 75: There was 1 warning 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: 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: 0.001 0.001 186.7 75: (ns/day) (hour/ns) 75: Performance: 1877.657 0.013 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: 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: 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: 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: 0.002 0.001 186.8 75: (ns/day) (hour/ns) 75: Performance: 1662.330 0.014 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: 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_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: 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: Generated 1 of the 1 non-bonded parameter combinations 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: 75: There were 2 notes 75: 75: There was 1 warning 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: 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: 0.002 0.001 188.2 75: (ns/day) (hour/ns) 75: Performance: 1736.601 0.014 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: 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: 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: 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: 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: 0.002 0.001 186.9 75: (ns/day) (hour/ns) 75: Performance: 1759.918 0.014 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 (33 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: 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: 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: 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: 0.002 0.001 189.9 75: (ns/day) (hour/ns) 75: Performance: 1535.159 0.016 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: 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: 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 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: There were 2 notes 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: 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: 0.002 0.001 187.4 75: (ns/day) (hour/ns) 75: Performance: 1643.263 0.015 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 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_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: 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: 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: 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 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: 0.002 0.001 186.2 75: (ns/day) (hour/ns) 75: Performance: 1784.645 0.013 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 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 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: Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 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: 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 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_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: Last energy frame read 4 time 0.016 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: Generated 1 of the 1 non-bonded parameter combinations 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: 0.002 0.001 186.0 75: (ns/day) (hour/ns) 75: Performance: 1717.478 0.014 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: 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: 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: 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: 0.001 0.001 185.2 75: (ns/day) (hour/ns) 75: Performance: 1826.443 0.013 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_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: 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_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: 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: 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: 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: 0.001 0.001 186.5 75: (ns/day) (hour/ns) 75: Performance: 1936.685 0.012 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (32 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 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: 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: 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: 0.002 0.001 190.6 75: (ns/day) (hour/ns) 75: Performance: 1603.277 0.015 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: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note 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: 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: 0.002 0.001 189.7 75: (ns/day) (hour/ns) 75: Performance: 1774.109 0.014 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 0.001 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 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_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: 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: 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 75: There were 2 notes 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: 0.002 0.001 187.1 75: (ns/day) (hour/ns) 75: Performance: 1816.481 0.013 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 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: 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: 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: 0.001 0.001 187.9 75: (ns/day) (hour/ns) 75: Performance: 2034.542 0.012 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: 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: 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: 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: 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: 0.002 0.001 188.2 75: (ns/day) (hour/ns) 75: Performance: 1819.969 0.013 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: 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: 38 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 186.9 75: (ns/day) (hour/ns) 75: Performance: 1815.143 0.013 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (31 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: 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 3 notes 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: 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: 0.002 0.001 191.2 75: (ns/day) (hour/ns) 75: Performance: 1494.927 0.016 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_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: 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: 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: Generated 1 of the 1 non-bonded parameter combinations 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 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: 0.001 0.001 189.0 75: (ns/day) (hour/ns) 75: Performance: 1991.464 0.012 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 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: 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 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: 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: 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 0.004 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: 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: 0.001 0.001 187.4 75: (ns/day) (hour/ns) 75: Performance: 1914.714 0.013 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 0.004 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_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: 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: 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: 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: 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: 0.002 0.001 187.6 75: (ns/day) (hour/ns) 75: Performance: 1774.109 0.014 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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: 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: 0.002 0.001 188.1 75: (ns/day) (hour/ns) 75: Performance: 1712.703 0.014 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: 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: 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: 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: 0.001 0.001 186.6 75: (ns/day) (hour/ns) 75: Performance: 1848.918 0.013 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 (31 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: 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: 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: 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: 0.002 0.001 189.9 75: (ns/day) (hour/ns) 75: Performance: 1383.315 0.017 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: 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 3 notes 75: 75: There was 1 warning 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: 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: 0.002 0.001 189.9 75: (ns/day) (hour/ns) 75: Performance: 1726.382 0.014 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 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 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_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 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_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: 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 3 notes 75: 75: There was 1 warning 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 0.004 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 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: 0.001 0.001 186.6 75: (ns/day) (hour/ns) 75: Performance: 2040.269 0.012 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 0.004 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 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 2 time 0.008 Reading energy frame 11 time 0.011 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 8 time 0.008 Reading energy frame 4 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 Reading energy frame 13 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 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 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: 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 3 notes 75: 75: There was 1 warning 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: 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: 0.002 0.001 187.5 75: (ns/day) (hour/ns) 75: Performance: 1834.875 0.013 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: 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_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: 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: 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: 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: 0.001 0.001 186.6 75: (ns/day) (hour/ns) 75: Performance: 1904.651 0.013 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: 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 3 notes 75: 75: There was 1 warning 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: 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: 0.002 0.001 184.3 75: (ns/day) (hour/ns) 75: Performance: 1196.697 0.020 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (34 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_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_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: 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: 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: 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: 0.002 0.001 177.0 75: (ns/day) (hour/ns) 75: Performance: 1207.486 0.020 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: 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: 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: 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: 0.002 0.001 188.5 75: (ns/day) (hour/ns) 75: Performance: 1396.802 0.017 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 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_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 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_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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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: 0.002 0.001 186.9 75: (ns/day) (hour/ns) 75: Performance: 1749.423 0.014 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 0.004 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_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 0.004 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_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: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note 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: 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: 0.002 0.001 185.2 75: (ns/day) (hour/ns) 75: Performance: 1772.068 0.014 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: There were 3 notes 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: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note 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: 75: Writing final coordinates. 75: 75: NOTE: 38 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 185.9 75: (ns/day) (hour/ns) 75: Performance: 1703.940 0.014 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: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 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_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: 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: 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: 0.002 0.001 185.0 75: (ns/day) (hour/ns) 75: Performance: 1670.896 0.014 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (34 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: 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: 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: 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: 0.002 0.001 188.6 75: (ns/day) (hour/ns) 75: Performance: 1373.446 0.017 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: 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 3 notes 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: 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: 0.002 0.001 188.9 75: (ns/day) (hour/ns) 75: Performance: 1602.860 0.015 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 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_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: 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 3 notes 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: 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: 0.001 0.001 184.4 75: (ns/day) (hour/ns) 75: Performance: 1915.012 0.013 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 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: 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 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_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: 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: 0.001 0.001 187.3 75: (ns/day) (hour/ns) 75: Performance: 1960.724 0.012 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: 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_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: 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: 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: 75: There were 3 notes 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: 0.002 0.001 188.1 75: (ns/day) (hour/ns) 75: Performance: 1741.264 0.014 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: 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_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: 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: 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: 38 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 187.5 75: (ns/day) (hour/ns) 75: Performance: 1821.314 0.013 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_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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (34 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: 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: 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: 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: 0.002 0.001 191.0 75: (ns/day) (hour/ns) 75: Performance: 1571.179 0.015 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_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: 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: 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: 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: 0.002 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1665.475 0.014 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 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_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 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: 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: 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: 0.001 0.001 186.1 75: (ns/day) (hour/ns) 75: Performance: 2003.445 0.012 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 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 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: 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: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 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 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: 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: 0.001 0.001 188.4 75: (ns/day) (hour/ns) 75: Performance: 1916.501 0.013 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: 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_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: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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: 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: 0.001 0.001 188.7 75: (ns/day) (hour/ns) 75: Performance: 1992.108 0.012 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: 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_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: 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: 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: 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: 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: 0.002 0.001 189.3 75: (ns/day) (hour/ns) 75: Performance: 1783.870 0.013 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (32 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 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: 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: 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: 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: 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: 0.002 0.001 190.2 75: (ns/day) (hour/ns) 75: Performance: 1420.474 0.017 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: 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: 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: 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: 0.002 0.001 189.3 75: (ns/day) (hour/ns) 75: Performance: 1610.613 0.015 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 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 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 2 time 0.002 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.003 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 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 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 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_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: 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: 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: 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: 0.001 0.001 190.5 75: (ns/day) (hour/ns) 75: Performance: 1874.515 0.013 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_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.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 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 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 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.016 Reading energy frame 16 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 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 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: 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: 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: 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: 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: 0.002 0.001 187.9 75: (ns/day) (hour/ns) 75: Performance: 1678.407 0.014 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: 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: 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: 75: There was 1 warning 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: 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: 0.001 0.001 186.5 75: (ns/day) (hour/ns) 75: Performance: 1835.422 0.013 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: 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: 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: 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: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 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: 75: Writing final coordinates. 75: 75: NOTE: 38 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 189.6 75: (ns/day) (hour/ns) 75: Performance: 1640.856 0.015 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 (31 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 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_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: 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: 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: 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: 0.002 0.001 190.0 75: (ns/day) (hour/ns) 75: Performance: 1465.064 0.016 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: 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 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: 0.002 0.001 191.9 75: (ns/day) (hour/ns) 75: Performance: 1537.458 0.016 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 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 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 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_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: 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: 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: 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: 0.002 0.001 188.9 75: (ns/day) (hour/ns) 75: Performance: 1704.411 0.014 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 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_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 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_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: 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: 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: 0.002 0.001 189.7 75: (ns/day) (hour/ns) 75: Performance: 1601.818 0.015 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: 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: 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: 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: 0.001 0.001 189.5 75: (ns/day) (hour/ns) 75: Performance: 1917.396 0.013 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: 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: 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: 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: 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: 0.001 0.001 189.2 75: (ns/day) (hour/ns) 75: Performance: 2065.927 0.012 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 (32 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: 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: 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: 0.9%. 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: 0.6%. 75: 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: 0.003 0.002 188.7 75: (ns/day) (hour/ns) 75: Performance: 957.804 0.025 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: 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: 1.9%. 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: 1.1%. 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: 0.002 0.001 188.9 75: (ns/day) (hour/ns) 75: Performance: 1148.829 0.021 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: 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: 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: 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: 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: 2.0%. 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: 1.2%. 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: 0.002 0.001 185.1 75: (ns/day) (hour/ns) 75: Performance: 1407.653 0.017 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 0.004 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_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 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_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: 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: 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: 4.8%. 75: The balanceable part of the MD step is 41%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.0%. 75: 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: 0.003 0.001 188.3 75: (ns/day) (hour/ns) 75: Performance: 1086.716 0.022 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: 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: 3.1%. 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: 1.7%. 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: 0.002 0.001 183.2 75: (ns/day) (hour/ns) 75: Performance: 1158.660 0.021 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: 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: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 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: 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: 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: 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: 3.6%. 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: 2.0%. 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: 0.002 0.001 184.6 75: (ns/day) (hour/ns) 75: Performance: 1134.234 0.021 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 (38 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: 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: 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: 1.0%. 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: 0.7%. 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: 0.003 0.001 185.1 75: (ns/day) (hour/ns) 75: Performance: 1010.845 0.024 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: 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: 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: 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 66%, 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: 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: 0.002 0.001 186.8 75: (ns/day) (hour/ns) 75: Performance: 1117.568 0.021 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 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 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 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 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_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: 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_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: 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: 2.4%. 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: 1.5%. 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: 0.002 0.001 186.3 75: (ns/day) (hour/ns) 75: Performance: 1170.659 0.021 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 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: 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: 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: 0.7%. 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: 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 0.001 186.1 75: (ns/day) (hour/ns) 75: Performance: 1027.965 0.023 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_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.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: 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: 1.4%. 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: 0.8%. 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: 0.003 0.001 185.4 75: (ns/day) (hour/ns) 75: Performance: 1082.705 0.022 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: 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: 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: Generated 1 of the 1 non-bonded parameter combinations 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: There were 3 notes 75: 75: There was 1 warning 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 turned on during the run due to measured imbalance. 75: Average load imbalance: 4.7%. 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: 3.0%. 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: 0.003 0.001 186.1 75: (ns/day) (hour/ns) 75: Performance: 1045.231 0.023 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 (35 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 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: 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: 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: 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: 0.003 0.001 184.8 75: (ns/day) (hour/ns) 75: Performance: 988.939 0.024 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: 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: 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: 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: 0.002 0.001 184.9 75: (ns/day) (hour/ns) 75: Performance: 1152.914 0.021 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 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 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 0 time 0.000 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 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 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 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 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_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: 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_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: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note 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_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: 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: 0.002 0.001 184.2 75: (ns/day) (hour/ns) 75: Performance: 1427.881 0.017 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_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.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 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 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 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 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 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 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 /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: 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_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: 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: 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: 0.002 0.001 182.3 75: (ns/day) (hour/ns) 75: Performance: 1195.419 0.020 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: 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: 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: 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: 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: 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: 0.002 0.001 183.4 75: (ns/day) (hour/ns) 75: Performance: 1266.179 0.019 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: 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: 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: 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: 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: 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: 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: 0.002 0.001 183.4 75: (ns/day) (hour/ns) 75: Performance: 1369.021 0.018 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: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (33 ms) 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: 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: 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: 0.003 0.001 185.6 75: (ns/day) (hour/ns) 75: Performance: 1011.011 0.024 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: 75: There were 2 notes 75: 75: There was 1 warning 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_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: 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: 0.002 0.001 185.6 75: (ns/day) (hour/ns) 75: Performance: 1233.599 0.019 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 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: Excluding 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_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: 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: 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 0.004 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 75: Writing final coordinates. 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: 0.003 0.001 180.6 75: (ns/day) (hour/ns) 75: Performance: 986.879 0.024 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 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 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 Last energy frame read 4 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 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_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: 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: 75: There was 1 warning 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_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: 13 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 184.5 75: (ns/day) (hour/ns) 75: Performance: 1125.839 0.021 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: 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: 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: 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: 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: 13 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 185.5 75: (ns/day) (hour/ns) 75: Performance: 1173.446 0.020 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: 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: 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: 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: 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: 0.002 0.001 184.3 75: (ns/day) (hour/ns) 75: Performance: 1154.967 0.021 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 (33 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 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_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: 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: 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: 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: 0.003 0.001 185.6 75: (ns/day) (hour/ns) 75: Performance: 1052.194 0.023 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: 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: 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: 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: 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: 0.002 0.001 186.0 75: (ns/day) (hour/ns) 75: Performance: 1208.908 0.020 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 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: 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: 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: 13 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 185.4 75: (ns/day) (hour/ns) 75: Performance: 1227.454 0.020 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_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 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 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 6 time 0.006 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 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 2 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 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 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: 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: 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: 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: 0.003 0.001 185.5 75: (ns/day) (hour/ns) 75: Performance: 1037.050 0.023 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: 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: 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: 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: 13 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.002 0.001 184.9 75: (ns/day) (hour/ns) 75: Performance: 1150.867 0.021 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_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: 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: 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: 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: 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: 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: 0.002 0.001 184.4 75: (ns/day) (hour/ns) 75: Performance: 1175.013 0.020 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 (33 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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: 0.003 0.002 188.6 75: (ns/day) (hour/ns) 75: Performance: 916.550 0.026 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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: 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: 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: 0.003 0.001 187.9 75: (ns/day) (hour/ns) 75: Performance: 1023.184 0.023 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: 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_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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 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: Reading energy frame 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 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: 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: 0.002 0.001 186.5 75: (ns/day) (hour/ns) 75: Performance: 1138.321 0.021 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: Reading energy frame 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_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: 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: 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: 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: 0.003 0.002 176.6 75: (ns/day) (hour/ns) 75: Performance: 898.832 0.027 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: 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_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: 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: 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: 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: 0.003 0.002 177.7 75: (ns/day) (hour/ns) 75: Performance: 892.646 0.027 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: 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_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: 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: 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: 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: 0.003 0.002 185.6 75: (ns/day) (hour/ns) 75: Performance: 956.540 0.025 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 (38 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: 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: 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 0.002 188.3 75: (ns/day) (hour/ns) 75: Performance: 664.717 0.036 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: 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: 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 0.002 188.2 75: (ns/day) (hour/ns) 75: Performance: 776.529 0.031 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 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 11 time 0.011 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 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 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 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 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: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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: 0.003 0.002 186.6 75: (ns/day) (hour/ns) 75: Performance: 864.038 0.028 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 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 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 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 0 time 0.000 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 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 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_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: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 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: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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: 0.003 0.002 187.2 75: (ns/day) (hour/ns) 75: Performance: 822.729 0.029 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: 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: 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 0.002 187.0 75: (ns/day) (hour/ns) 75: Performance: 775.503 0.031 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: 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_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: 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: 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: 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: 0.003 0.002 186.3 75: (ns/day) (hour/ns) 75: Performance: 828.594 0.029 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (39 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 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_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: 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: 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: 0.003 0.002 186.3 75: (ns/day) (hour/ns) 75: Performance: 879.833 0.027 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_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: 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: 75: There were 2 notes 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: Note 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: 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: 0.003 0.002 187.4 75: (ns/day) (hour/ns) 75: Performance: 867.811 0.028 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 0.001 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_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 0.001 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_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: Number of degrees of freedom in T-Coupling group System is 33.00 75: Excluding 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: There were 2 notes 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: 0.003 0.001 184.7 75: (ns/day) (hour/ns) 75: Performance: 1027.451 0.023 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 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: 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: 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: 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: 0.003 0.002 185.7 75: (ns/day) (hour/ns) 75: Performance: 920.522 0.026 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: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 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: 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: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that 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: 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: 0.003 0.002 186.3 75: (ns/day) (hour/ns) 75: Performance: 938.686 0.026 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: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 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: 0.003 0.002 184.5 75: (ns/day) (hour/ns) 75: Performance: 953.283 0.025 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 (36 ms) 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (751 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 22 tests from 1 test suite ran. (761 ms total) 75: [ PASSED ] 22 tests. 75/81 Test #75: MdrunMpiCoordinationCouplingTestsTwoRanks ...... Passed 0.90 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: 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: 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: This run will generate roughly 0 Mb of data 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: 0.001 0.001 95.6 76: (ns/day) (hour/ns) 76: Performance: 1775.899 0.014 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: 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: 0.001 0.001 93.6 76: (ns/day) (hour/ns) 76: Performance: 2134.648 0.011 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: 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: 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: 0.000 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2844.226 0.008 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: 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_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: 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: 0.001 0.001 93.9 76: (ns/day) (hour/ns) 76: Performance: 2254.976 0.011 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: 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: 0.001 0.001 94.9 76: (ns/day) (hour/ns) 76: Performance: 2008.671 0.012 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: 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: 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: 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_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: 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: 0.001 0.001 94.6 76: (ns/day) (hour/ns) 76: Performance: 2233.718 0.011 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 (818 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: 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 95.4 76: (ns/day) (hour/ns) 76: Performance: 1707.009 0.014 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: 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: 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: 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: 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 94.7 76: (ns/day) (hour/ns) 76: Performance: 2083.393 0.012 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: 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: 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 94.4 76: (ns/day) (hour/ns) 76: Performance: 2648.579 0.009 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: 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: 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: 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: 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 94.3 76: (ns/day) (hour/ns) 76: Performance: 2250.034 0.011 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: 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: 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 94.2 76: (ns/day) (hour/ns) 76: Performance: 2450.515 0.010 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: 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: 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: 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 94.9 76: (ns/day) (hour/ns) 76: Performance: 1878.230 0.013 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (797 ms) 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: [ 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: 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 95.8 76: (ns/day) (hour/ns) 76: Performance: 1751.164 0.014 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: 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: 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 94.8 76: (ns/day) (hour/ns) 76: Performance: 2158.582 0.011 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: 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_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: 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: 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 94.1 76: (ns/day) (hour/ns) 76: Performance: 2330.909 0.010 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: 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: 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: 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 94.5 76: (ns/day) (hour/ns) 76: Performance: 1912.040 0.013 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: 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: 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: 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 94.5 76: (ns/day) (hour/ns) 76: Performance: 2236.962 0.011 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: 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: 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: 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 94.5 76: (ns/day) (hour/ns) 76: Performance: 2316.884 0.010 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (798 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 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_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: 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: 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: 0.001 0.001 95.8 76: (ns/day) (hour/ns) 76: Performance: 1605.994 0.015 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: 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: 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: This run will generate roughly 0 Mb of data 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: 0.001 0.001 94.7 76: (ns/day) (hour/ns) 76: Performance: 1995.011 0.012 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: 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: 0.001 0.001 93.7 76: (ns/day) (hour/ns) 76: Performance: 2247.572 0.011 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: 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_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: 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: 0.001 0.001 94.4 76: (ns/day) (hour/ns) 76: Performance: 2186.158 0.011 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: 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: 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: 0.001 0.001 94.5 76: (ns/day) (hour/ns) 76: Performance: 1987.288 0.012 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: 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_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: 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: 0.001 0.001 93.9 76: (ns/day) (hour/ns) 76: Performance: 2010.638 0.012 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 (804 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: 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: 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: 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: 0.001 0.001 95.4 76: (ns/day) (hour/ns) 76: Performance: 1894.984 0.013 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: 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: 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: 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: 0.001 0.001 94.3 76: (ns/day) (hour/ns) 76: Performance: 1933.645 0.012 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: 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: 0.001 0.001 94.2 76: (ns/day) (hour/ns) 76: Performance: 2251.679 0.011 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: 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: 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: 0.001 0.001 94.3 76: (ns/day) (hour/ns) 76: Performance: 2133.170 0.011 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: 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: 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: 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: 0.001 0.001 90.9 76: (ns/day) (hour/ns) 76: Performance: 1962.598 0.012 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: 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: 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: 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: 0.001 0.001 93.7 76: (ns/day) (hour/ns) 76: Performance: 2079.876 0.012 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (819 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 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_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: 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: There were 3 notes 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: 0.001 0.001 95.3 76: (ns/day) (hour/ns) 76: Performance: 1542.848 0.016 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: 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: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 2232.908 0.011 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: 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: 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: 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: 0.001 0.001 95.1 76: (ns/day) (hour/ns) 76: Performance: 1996.951 0.012 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: 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: 0.001 0.001 93.2 76: (ns/day) (hour/ns) 76: Performance: 1939.734 0.012 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: 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: 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: 0.001 0.001 95.7 76: (ns/day) (hour/ns) 76: Performance: 1906.714 0.013 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: 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_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: 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: 0.001 0.001 96.1 76: (ns/day) (hour/ns) 76: Performance: 2052.163 0.012 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 (842 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: 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: 0.001 0.001 96.0 76: (ns/day) (hour/ns) 76: Performance: 1643.702 0.015 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: 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: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 1781.548 0.013 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: 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: 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: 0.001 0.001 93.8 76: (ns/day) (hour/ns) 76: Performance: 2010.638 0.012 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: 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: 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: 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: 0.001 0.001 95.5 76: (ns/day) (hour/ns) 76: Performance: 1878.803 0.013 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: 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: 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: 0.001 0.001 95.0 76: (ns/day) (hour/ns) 76: Performance: 1854.483 0.013 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: 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: 0.001 0.001 95.6 76: (ns/day) (hour/ns) 76: Performance: 2128.747 0.011 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: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (813 ms) 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: 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: 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: 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: 0.001 0.001 97.5 76: (ns/day) (hour/ns) 76: Performance: 1195.767 0.020 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: 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: 0.001 0.001 97.3 76: (ns/day) (hour/ns) 76: Performance: 1485.196 0.016 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: 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: 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_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/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: 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: 0.001 0.001 97.2 76: (ns/day) (hour/ns) 76: Performance: 1378.517 0.017 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: 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_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/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: 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: 0.001 0.001 96.9 76: (ns/day) (hour/ns) 76: Performance: 1650.306 0.015 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: 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: 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: 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: 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: 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: 0.001 0.001 97.1 76: (ns/day) (hour/ns) 76: Performance: 1477.361 0.016 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: 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: 0.001 0.001 96.8 76: (ns/day) (hour/ns) 76: Performance: 1499.658 0.016 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 (821 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: 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: 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: 0.001 0.001 97.1 76: (ns/day) (hour/ns) 76: Performance: 1439.727 0.017 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: 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: There were 3 notes 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: 0.001 0.001 96.9 76: (ns/day) (hour/ns) 76: Performance: 1544.396 0.016 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: 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: 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: 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: 0.001 0.001 95.3 76: (ns/day) (hour/ns) 76: Performance: 1692.006 0.014 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: 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: 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: 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: 0.001 0.001 96.8 76: (ns/day) (hour/ns) 76: Performance: 1745.211 0.014 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: 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: 76: This run will generate roughly 0 Mb of data 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1836.243 0.013 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: 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: 0.001 0.001 97.1 76: (ns/day) (hour/ns) 76: Performance: 1584.515 0.015 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: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (792 ms) 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: 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: 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: 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: 0.001 0.001 97.1 76: (ns/day) (hour/ns) 76: Performance: 1273.113 0.019 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: 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: 0.001 0.001 96.5 76: (ns/day) (hour/ns) 76: Performance: 1510.320 0.016 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: 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: 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1626.774 0.015 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: 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_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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1570.378 0.015 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: 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: There were 3 notes 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: 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: 0.001 0.001 96.7 76: (ns/day) (hour/ns) 76: Performance: 1521.510 0.016 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: 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: 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: 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: 0.001 0.001 97.1 76: (ns/day) (hour/ns) 76: Performance: 1573.185 0.015 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: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (789 ms) 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (8099 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 10 tests from 1 test suite ran. (8107 ms total) 76: [ PASSED ] 10 tests. 76/81 Test #76: MdrunMpiCoordinationConstraintsTestsOneRank .... Passed 8.25 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: Generating 1-4 interactions: fudge = 0.5 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: 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: There were 4 notes 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: 0.6%. 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: 0.3%. 77: 77: 77: NOTE: 11 % of the run time was spent in domain decomposition, 77: 3 % 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: 0.002 0.001 192.8 77: (ns/day) (hour/ns) 77: Performance: 1159.859 0.021 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: 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: There were 4 notes 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: 1.2%. 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: 0.6%. 77: 77: 77: NOTE: 11 % of the run time was spent in domain decomposition, 77: 3 % 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: 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: 0.002 0.001 191.4 77: (ns/day) (hour/ns) 77: Performance: 1348.346 0.018 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_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.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: 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: 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: 2.1%. 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: 1.0%. 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: 0.002 0.001 189.9 77: (ns/day) (hour/ns) 77: Performance: 1629.787 0.015 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 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: 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: 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: 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: 77: This run will generate roughly 0 Mb of data 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: 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: 16 steps, 0.0 ps. 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: 4.4%. 77: The balanceable part of the MD step is 49%, 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: 15 % of the run time was spent in domain decomposition, 77: 3 % 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: 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: 0.002 0.001 190.5 77: (ns/day) (hour/ns) 77: Performance: 1544.589 0.016 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: 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: 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: 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: 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: 3.0%. 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: 1.5%. 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: 0.002 0.001 187.7 77: (ns/day) (hour/ns) 77: Performance: 1563.602 0.015 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: 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: 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: 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: 0.9%. 77: The balanceable part of the MD step is 48%, 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: 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: 0.002 0.001 188.2 77: (ns/day) (hour/ns) 77: Performance: 1794.261 0.013 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: 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 (820 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: 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: 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: 0.4%. 77: The balanceable part of the MD step is 60%, 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: 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: 0.002 0.001 192.4 77: (ns/day) (hour/ns) 77: Performance: 1187.699 0.020 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: 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_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: 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: 1.0%. 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: 0.6%. 77: 77: 77: NOTE: 11 % of the run time was spent in domain decomposition, 77: 3 % 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: 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: 0.002 0.001 190.4 77: (ns/day) (hour/ns) 77: Performance: 1387.677 0.017 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_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 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 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 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 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 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 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 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 8 time 0.008 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 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 16 time 0.016 Last energy frame read 16 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 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: 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: 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: 1.4%. 77: The balanceable part of the MD step is 52%, 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: 11 % of the run time was spent in domain decomposition, 77: 4 % 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: 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: 0.002 0.001 185.2 77: (ns/day) (hour/ns) 77: Performance: 1554.724 0.015 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_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 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 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.003 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 3 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 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 16 time 0.016 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 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: 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_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: 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: 1.4%. 77: The balanceable part of the MD step is 52%, 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: 10 % of the run time was spent in domain decomposition, 77: 4 % 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: 0.002 0.001 188.0 77: (ns/day) (hour/ns) 77: Performance: 1552.178 0.015 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: 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: 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_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: 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: 1.6%. 77: The balanceable part of the MD step is 47%, 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: 11 % of the run time was spent in domain decomposition, 77: 3 % 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: 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: 0.002 0.001 186.5 77: (ns/day) (hour/ns) 77: Performance: 1414.440 0.017 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_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.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: 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: 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: 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: 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: 0.2%. 77: The balanceable part of the MD step is 48%, 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: 11 % of the run time was spent in domain decomposition, 77: 3 % 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: 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: 0.002 0.001 188.5 77: (ns/day) (hour/ns) 77: Performance: 1449.893 0.017 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 (810 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: 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: 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: 13 % 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: 0.002 0.001 190.6 77: (ns/day) (hour/ns) 77: Performance: 1297.513 0.018 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: 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: There were 3 notes 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: 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: 0.002 0.001 190.3 77: (ns/day) (hour/ns) 77: Performance: 1469.432 0.016 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_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 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: 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: 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: 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: 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: 0.001 0.001 189.1 77: (ns/day) (hour/ns) 77: Performance: 1906.124 0.013 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 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 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 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 2 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 5 time 0.005 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 4 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 13 time 0.013 Reading energy frame 14 time 0.014 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 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: 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_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: 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: 8 % 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: 0.002 0.001 189.3 77: (ns/day) (hour/ns) 77: Performance: 1597.457 0.015 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: 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: 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: 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: 0.002 0.001 190.9 77: (ns/day) (hour/ns) 77: Performance: 1326.428 0.018 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: 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: 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: 0.002 0.001 185.9 77: (ns/day) (hour/ns) 77: Performance: 1543.235 0.016 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: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (802 ms) 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: [ 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: 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: 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: 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: 0.002 0.001 191.0 77: (ns/day) (hour/ns) 77: Performance: 1256.239 0.019 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: 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: 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: 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: 0.002 0.001 188.9 77: (ns/day) (hour/ns) 77: Performance: 1505.154 0.016 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 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_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: 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: 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: NOTE: 8 % 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: 0.002 0.001 188.7 77: (ns/day) (hour/ns) 77: Performance: 1680.697 0.014 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: 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: Reading energy frame 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/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: 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 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Last energy frame read 4 time 0.016 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: 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: 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: 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: 0.002 0.001 188.2 77: (ns/day) (hour/ns) 77: Performance: 1591.679 0.015 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: 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: 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: 0.002 0.001 184.2 77: (ns/day) (hour/ns) 77: Performance: 1618.653 0.015 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: 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: 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: 0.002 0.001 187.4 77: (ns/day) (hour/ns) 77: Performance: 1475.415 0.016 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: 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 (803 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: 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: 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: 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: 0.002 0.001 188.3 77: (ns/day) (hour/ns) 77: Performance: 1331.157 0.018 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: 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: 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: 8 % 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: 0.002 0.001 189.6 77: (ns/day) (hour/ns) 77: Performance: 1522.074 0.016 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 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 16 time 0.016 Last energy frame read 16 time 0.016 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: 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: Number of degrees of freedom in T-Coupling group System is 27.00 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: 77: There were 3 notes 77: This run will generate roughly 0 Mb of data 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: 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 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: 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: 0.001 0.001 188.6 77: (ns/day) (hour/ns) 77: Performance: 1889.753 0.013 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: 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: 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: 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: 0.002 0.001 188.9 77: (ns/day) (hour/ns) 77: Performance: 1558.263 0.015 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: 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: 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_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: 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: 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: 0.002 0.001 187.2 77: (ns/day) (hour/ns) 77: Performance: 1505.337 0.016 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: This run will generate roughly 0 Mb of data 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: There were 3 notes 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: 8 % 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: 0.002 0.001 187.0 77: (ns/day) (hour/ns) 77: Performance: 1591.679 0.015 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 (805 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: 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: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 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: 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: 0.002 0.001 192.1 77: (ns/day) (hour/ns) 77: Performance: 1348.937 0.018 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: This run will generate roughly 0 Mb of data 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: There were 3 notes 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: 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: 0.003 0.001 192.5 77: (ns/day) (hour/ns) 77: Performance: 1125.325 0.021 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 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: 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/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.001 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.002 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 13 time 0.013 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 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: This run will generate roughly 0 Mb of data 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: 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: 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: 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: 0.002 0.001 186.0 77: (ns/day) (hour/ns) 77: Performance: 1352.639 0.018 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: 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 Reading energy frame 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 Last energy frame read 4 time 0.016 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: 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_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: 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: 0.002 0.001 188.9 77: (ns/day) (hour/ns) 77: Performance: 1683.912 0.014 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_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: 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: 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: 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_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/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: 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: 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: 0.003 0.002 193.6 77: (ns/day) (hour/ns) 77: Performance: 913.357 0.026 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: 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: 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_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/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: 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: 0.002 0.001 190.8 77: (ns/day) (hour/ns) 77: Performance: 1615.046 0.015 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (836 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 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: 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_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: 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: 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: 0.002 0.001 191.5 77: (ns/day) (hour/ns) 77: Performance: 1252.917 0.019 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: 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: 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: 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: 0.002 0.001 190.8 77: (ns/day) (hour/ns) 77: Performance: 1394.273 0.017 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 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 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 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 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 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 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 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 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 6 time 0.006 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 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 13 time 0.013 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 14 time 0.014 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 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 15 time 0.015 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 13 time 0.013 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 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: 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: 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: 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 starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 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: 0.002 0.001 190.1 77: (ns/day) (hour/ns) 77: Performance: 1573.587 0.015 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: 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: 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: 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: 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: 0.002 0.001 190.1 77: (ns/day) (hour/ns) 77: Performance: 1436.706 0.017 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: 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: 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: 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: 0.002 0.001 191.7 77: (ns/day) (hour/ns) 77: Performance: 1399.340 0.017 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: 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: 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: 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: 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: 0.002 0.001 190.6 77: (ns/day) (hour/ns) 77: Performance: 1417.858 0.017 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: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (837 ms) 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: 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: 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: 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: 0.8%. 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: 0.5%. 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: 0.003 0.002 187.1 77: (ns/day) (hour/ns) 77: Performance: 877.953 0.027 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: 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: 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: 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: 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: 0.003 0.002 187.6 77: (ns/day) (hour/ns) 77: Performance: 948.002 0.025 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 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: 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 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 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 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 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 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 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.004 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 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 14 time 0.014 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 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 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 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: 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_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: 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 60%, 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: 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: 0.002 0.001 184.8 77: (ns/day) (hour/ns) 77: Performance: 1207.723 0.020 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: Reading energy frame 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 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 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 1 time 0.004 Reading energy frame 1 time 0.001 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 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 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 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 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 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: 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: 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_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: 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: 2.3%. 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: 1.3%. 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: 0.003 0.001 184.6 77: (ns/day) (hour/ns) 77: Performance: 1072.620 0.022 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: 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: This run will generate roughly 0 Mb of data 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 got disabled because it was unsuitable to use. 77: Average load imbalance: 3.7%. 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: 2.0%. 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: 0.003 0.001 185.3 77: (ns/day) (hour/ns) 77: Performance: 1027.793 0.023 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: 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_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: 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: 3.3%. 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: 1.9%. 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: 0.002 0.001 184.5 77: (ns/day) (hour/ns) 77: Performance: 1100.794 0.022 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: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (825 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: 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: NOTE: 8 % 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: 0.003 0.002 186.6 77: (ns/day) (hour/ns) 77: Performance: 863.917 0.028 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: 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: 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: 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: NOTE: 8 % 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: 0.003 0.002 185.4 77: (ns/day) (hour/ns) 77: Performance: 957.804 0.025 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: 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 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 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 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 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 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 11 time 0.011 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 12 time 0.012 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 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 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: 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: Number of degrees of freedom in T-Coupling group System is 27.00 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: 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: 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: 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: 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: 0.002 0.001 185.2 77: (ns/day) (hour/ns) 77: Performance: 1183.478 0.020 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_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 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 1 time 0.004 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 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 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 2 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 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 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 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 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 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: 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: 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: 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: 77: This run will generate roughly 0 Mb of data 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: NOTE: 8 % 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: 0.003 0.001 184.0 77: (ns/day) (hour/ns) 77: Performance: 990.768 0.024 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: 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: 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: 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: 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: NOTE: 8 % 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: 0.003 0.002 183.8 77: (ns/day) (hour/ns) 77: Performance: 972.623 0.025 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: 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: 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: 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: NOTE: 8 % 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: 0.003 0.002 184.5 77: (ns/day) (hour/ns) 77: Performance: 938.185 0.026 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: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (828 ms) 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: 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: 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: 8 % 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 0.002 186.6 77: (ns/day) (hour/ns) 77: Performance: 772.730 0.031 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: 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: 8 % 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: 0.003 0.002 184.6 77: (ns/day) (hour/ns) 77: Performance: 953.357 0.025 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: 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 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 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 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 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 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 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 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 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 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 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 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 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: 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: 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: 8 % 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: 0.003 0.001 184.3 77: (ns/day) (hour/ns) 77: Performance: 1009.024 0.024 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: Reading energy frame 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 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: 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: 8 % 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: 0.003 0.002 185.3 77: (ns/day) (hour/ns) 77: Performance: 967.658 0.025 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: 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: 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: 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: 0.003 0.002 184.3 77: (ns/day) (hour/ns) 77: Performance: 931.941 0.026 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: There were 3 notes 77: 77: This run will generate roughly 0 Mb of data 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: 8 % 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: 0.003 0.002 184.6 77: (ns/day) (hour/ns) 77: Performance: 970.249 0.025 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_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.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (823 ms) 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (8195 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 10 tests from 1 test suite ran. (8205 ms total) 77: [ PASSED ] 10 tests. 77/81 Test #77: MdrunMpiCoordinationConstraintsTestsTwoRanks ... Passed 8.37 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: 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 -1350599041 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: 0.044 0.022 199.5 78: (ns/day) (hour/ns) 78: Performance: 81.685 0.294 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 (9742 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: 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 -268472592 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: 0.095 0.048 199.8 78: (ns/day) (hour/ns) 78: Performance: 38.180 0.629 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 (63 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: 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 -270544965 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: 0.069 0.035 199.7 78: (ns/day) (hour/ns) 78: Performance: 52.265 0.459 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 (51 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: 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 -151330342 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: 0.274 0.137 199.9 78: (ns/day) (hour/ns) 78: Performance: 63.787 0.376 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 (154 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: 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 -1933641029 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: 0.95 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: 0.072 0.036 199.7 78: (ns/day) (hour/ns) 78: Performance: 50.009 0.480 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 (51 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: 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 922185687 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: 0.076 0.038 199.7 78: (ns/day) (hour/ns) 78: Performance: 47.568 0.505 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 (53 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: 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 -1107492867 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: 0.89 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: 0.021 0.010 199.0 78: (ns/day) (hour/ns) 78: Performance: 173.708 0.138 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 (23 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: 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: 0.021 0.011 198.9 78: (ns/day) (hour/ns) 78: Performance: 168.444 0.142 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 -805935363 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: 0.90 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (23 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: 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 -84429905 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: 0.95 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: 0.057 0.029 199.7 78: (ns/day) (hour/ns) 78: Performance: 63.483 0.378 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 (43 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: 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 -842559510 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: 0.90 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: 0.027 0.014 199.2 78: (ns/day) (hour/ns) 78: Performance: 132.353 0.181 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 (26 ms) 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest (10234 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 10 tests from 1 test suite ran. (10240 ms total) 78: [ PASSED ] 10 tests. 78/81 Test #78: MdrunFEPTests .................................. Passed 10.41 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: 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: NOTE: 23 % 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: 0.041 0.021 199.0 79: (ns/day) (hour/ns) 79: Performance: 88.365 0.272 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 (199 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: 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: NOTE: 17 % 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: 0.037 0.019 199.5 79: (ns/day) (hour/ns) 79: Performance: 97.084 0.247 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 (231 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: 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: 17 % 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: 0.035 0.017 199.5 79: (ns/day) (hour/ns) 79: Performance: 103.695 0.231 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 (162 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: 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: 17 % 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: 0.035 0.017 199.4 79: (ns/day) (hour/ns) 79: Performance: 104.032 0.231 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 (155 ms) 79: [----------] 4 tests from PullTest/PullIntegrationTest (748 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 4 tests from 1 test suite ran. (755 ms total) 79: [ PASSED ] 4 tests. 79/81 Test #79: MdrunPullTests ................................. Passed 0.94 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 0.19 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: 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: 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: 81: There were 4 notes 81: 81: This run will generate roughly 0 Mb of data 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: 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: 33.1%. 81: The balanceable part of the MD step is 34%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 11.4%. 81: 81: NOTE: 11.4 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 39 % 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: 0.006 0.003 194.0 81: (ns/day) (hour/ns) 81: Performance: 246.095 0.098 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: 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: 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 virtual site types... 81: 81: Reading virtual site types... 81: trr version: GMX_trn_file (single precision) 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (14 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/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: 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: 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: This run will generate roughly 0 Mb of data 81: 81: There were 4 notes 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: 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: 32.3%. 81: The balanceable part of the MD step is 37%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 12.1%. 81: 81: NOTE: 12.1 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 81: 81: NOTE: 10 % 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: 22 % 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 0.002 190.4 81: (ns/day) (hour/ns) 81: Performance: 372.295 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: 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: Reading virtual site types... 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (11 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 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: 0.002 0.001 183.5 81: (ns/day) (hour/ns) 81: Performance: 592.352 0.041 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 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: Reading virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (10 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 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: 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: Number of degrees of freedom in T-Coupling group System is 45.00 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: 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: 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: 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: 0.002 0.001 185.5 81: (ns/day) (hour/ns) 81: Performance: 697.272 0.034 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: Reading virtual site types... 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (9 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: 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: 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: Number of degrees of freedom in T-Coupling group System is 45.00 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: 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: 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: 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: 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: 0.002 0.001 187.1 81: (ns/day) (hour/ns) 81: Performance: 690.117 0.035 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: 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: Reading virtual site types... 81: 81: Reading virtual site types... 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (8 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 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: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: There were 5 notes 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: 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: 0.002 0.001 184.8 81: (ns/day) (hour/ns) 81: Performance: 688.006 0.035 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: Reading virtual site types... 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 virtual site types... 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (9 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 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: 0.002 0.001 187.7 81: (ns/day) (hour/ns) 81: Performance: 698.467 0.034 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 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: 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: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (7 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 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: 0.002 0.001 180.1 81: (ns/day) (hour/ns) 81: Performance: 751.755 0.032 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: Reading virtual site types... 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: Reading virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (7 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: 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: 81: This run will generate roughly 0 Mb of data 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: 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: 11.8%. 81: The balanceable part of the MD step is 43%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 5.0%. 81: 81: NOTE: 5.0 % of the available CPU time was lost due to load imbalance 81: in the domain decomposition. 81: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 81: You can also consider manually changing the decomposition (option -dd); 81: e.g. by using fewer domains along the box dimension in which there is 81: considerable inhomogeneity in the simulated system. 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: 0.002 0.001 189.7 81: (ns/day) (hour/ns) 81: Performance: 740.071 0.032 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: 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: Reading virtual site types... 81: Reading virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (6 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 81: NOTE: 32 % 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: 0.002 0.001 188.5 81: (ns/day) (hour/ns) 81: Performance: 743.784 0.032 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 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: Reading virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (7 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 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: 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 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: 0.002 0.001 190.0 81: (ns/day) (hour/ns) 81: Performance: 650.671 0.037 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: 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: Reading virtual site types... 81: Reading virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (7 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 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: 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: 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: 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: 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: 32 % 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: 0.002 0.001 190.9 81: (ns/day) (hour/ns) 81: Performance: 725.017 0.033 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: 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 virtual site types... 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 virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (7 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 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: 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 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: 0.002 0.001 189.7 81: (ns/day) (hour/ns) 81: Performance: 716.496 0.033 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 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: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (6 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: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 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: 0.002 0.001 188.0 81: (ns/day) (hour/ns) 81: Performance: 870.892 0.028 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 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: 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: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (6 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: 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 14 % 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: 26 % 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: 0.002 0.001 187.0 81: (ns/day) (hour/ns) 81: Performance: 827.160 0.029 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 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: Reading virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (6 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: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: Number of degrees of freedom in T-Coupling group System is 45.00 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: 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: 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: 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: 0.002 0.001 183.7 81: (ns/day) (hour/ns) 81: Performance: 833.076 0.029 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 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: Reading virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (6 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/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: 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 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: 0.002 0.001 189.7 81: (ns/day) (hour/ns) 81: Performance: 960.816 0.025 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 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: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (6 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 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: 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: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 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: 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: 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: 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: 0.002 0.001 189.8 81: (ns/day) (hour/ns) 81: Performance: 886.154 0.027 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 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: Reading virtual site types... 81: 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (6 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: 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: 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: 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: 0.002 0.001 189.2 81: (ns/day) (hour/ns) 81: Performance: 956.449 0.025 81: Reading virtual site types... 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (6 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 (155 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 37 tests from 2 test suites ran. (172 ms total) 81: [ PASSED ] 37 tests. 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 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 0.34 sec 100% tests passed, 0 tests failed out of 81 Label Time Summary: GTest = 263.92 sec*proc (79 tests) IntegrationTest = 229.80 sec*proc (23 tests) MpiTest = 175.64 sec*proc (19 tests) QuickGpuTest = 4.85 sec*proc (15 tests) SlowTest = 27.12 sec*proc (13 tests) UnitTest = 6.99 sec*proc (43 tests) Total Test time (real) = 264.06 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 - not 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 - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/aarch64-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 - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- 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/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-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/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-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 -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2022.5/build/documentation /usr/bin/make -j12 manual -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' /usr/bin/cmake -S/build/reproducible-path/gromacs-2022.5 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/build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/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/documentation/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/documentation/src/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/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 -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -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/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/external/zlib -isystem /build/reproducible-path/gromacs-2022.5/src/external -g 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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/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/p2p_wait.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' 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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/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 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/collective.cpp [ 1%] Built target gmx_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.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/linearalgebra /build/reproducible-path/gromacs-2022.5/build/documentation /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2022.5/build/documentation/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 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/reduce.cpp 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 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/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 [ 1%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/external/zlib -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 -fPIC -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/external/zlib/trees.c /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_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/mdrun_objlib.dir/DependInfo.cmake --color= 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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/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 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/event.cpp make[4]: Leaving 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'/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/src/gromacs && /usr/bin/c++ -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/documentation/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 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/numa_malloc.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 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/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 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/once.cpp 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 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-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 /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.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-rst.dir/DependInfo.cmake --color= 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 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-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/documentation/api/legacy/include -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 -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 -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -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/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/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/cmake -E copy 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/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/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/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/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/gmxtree.rst 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/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/muParserCallback.cpp.o -MF CMakeFiles/muparser.dir/src/muParserCallback.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/muparser/src/muParserCallback.cpp 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 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/jenkins.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/jenkins.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/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 [ 4%] Built target thread_mpi cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/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/documentation/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/documentation/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/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/documentation/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/documentation/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 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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-redundant-move -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -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 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 /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /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/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/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation && /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/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-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/aarch64-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/aarch64-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/aarch64-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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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-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) | ^~~~~~ /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) | ^~~~~~ 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 = 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) | ^~~~~~ /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/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 = 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) | ^~~~~~ /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) | ^~~~~~ 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 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 /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/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 = 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 -DTMPI_EXPORTS -DTMPI_USE_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 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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